From 906577873b66253b0d244871bfec2eeeaff73053 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Mon, 27 Sep 2021 10:41:24 +0200 Subject: [PATCH] Bulk update modules to use versions.yml (#739) * New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel --- modules/abacas/functions.nf | 58 +++++++++++-------- modules/abacas/main.nf | 9 ++- modules/abacas/meta.yml | 2 +- modules/adapterremoval/functions.nf | 58 +++++++++++-------- modules/adapterremoval/main.nf | 19 ++++-- modules/adapterremoval/meta.yml | 2 +- modules/agrvate/functions.nf | 58 +++++++++++-------- modules/agrvate/main.nf | 9 ++- modules/agrvate/meta.yml | 2 +- modules/allelecounter/functions.nf | 58 +++++++++++-------- modules/allelecounter/main.nf | 9 ++- modules/allelecounter/meta.yml | 2 +- modules/arriba/functions.nf | 58 +++++++++++-------- modules/arriba/main.nf | 9 ++- modules/arriba/meta.yml | 2 +- modules/artic/guppyplex/functions.nf | 58 +++++++++++-------- modules/artic/guppyplex/main.nf | 9 ++- modules/artic/guppyplex/meta.yml | 2 +- modules/artic/minion/functions.nf | 58 +++++++++++-------- modules/artic/minion/main.nf | 9 ++- modules/artic/minion/meta.yml | 2 +- modules/bamaligncleaner/functions.nf | 58 +++++++++++-------- modules/bamaligncleaner/main.nf | 9 ++- modules/bamaligncleaner/meta.yml | 2 +- modules/bandage/image/functions.nf | 58 +++++++++++-------- modules/bandage/image/main.nf | 9 ++- modules/bandage/image/meta.yml | 2 +- modules/bbmap/align/functions.nf | 58 +++++++++++-------- modules/bbmap/align/main.nf | 9 ++- modules/bbmap/align/meta.yml | 2 +- modules/bbmap/bbduk/functions.nf | 58 +++++++++++-------- modules/bbmap/bbduk/main.nf | 9 ++- modules/bbmap/bbduk/meta.yml | 2 +- modules/bbmap/index/functions.nf | 58 +++++++++++-------- modules/bbmap/index/main.nf | 9 ++- modules/bbmap/index/meta.yml | 2 +- modules/bcftools/concat/functions.nf | 58 +++++++++++-------- modules/bcftools/concat/main.nf | 9 ++- modules/bcftools/concat/meta.yml | 2 +- modules/bcftools/consensus/functions.nf | 58 +++++++++++-------- modules/bcftools/consensus/main.nf | 9 ++- modules/bcftools/consensus/meta.yml | 2 +- modules/bcftools/filter/functions.nf | 58 +++++++++++-------- modules/bcftools/filter/main.nf | 9 ++- modules/bcftools/filter/meta.yml | 2 +- modules/bcftools/isec/functions.nf | 58 +++++++++++-------- modules/bcftools/isec/main.nf | 9 ++- modules/bcftools/isec/meta.yml | 2 +- modules/bcftools/merge/functions.nf | 58 +++++++++++-------- modules/bcftools/merge/main.nf | 9 ++- modules/bcftools/merge/meta.yml | 2 +- modules/bcftools/mpileup/functions.nf | 58 +++++++++++-------- modules/bcftools/mpileup/main.nf | 9 ++- modules/bcftools/mpileup/meta.yml | 2 +- modules/bcftools/norm/functions.nf | 58 +++++++++++-------- modules/bcftools/norm/main.nf | 9 ++- modules/bcftools/norm/meta.yml | 2 +- modules/bcftools/query/functions.nf | 58 +++++++++++-------- modules/bcftools/query/main.nf | 9 ++- modules/bcftools/query/meta.yml | 2 +- modules/bcftools/reheader/functions.nf | 58 +++++++++++-------- modules/bcftools/reheader/main.nf | 9 ++- modules/bcftools/reheader/meta.yml | 2 +- modules/bcftools/stats/functions.nf | 58 +++++++++++-------- modules/bcftools/stats/main.nf | 9 ++- modules/bcftools/stats/meta.yml | 2 +- modules/bcftools/view/functions.nf | 58 +++++++++++-------- modules/bcftools/view/main.nf | 9 ++- modules/bcftools/view/meta.yml | 2 +- modules/bedtools/bamtobed/functions.nf | 58 +++++++++++-------- modules/bedtools/bamtobed/main.nf | 9 ++- modules/bedtools/bamtobed/meta.yml | 2 +- modules/bedtools/complement/functions.nf | 58 +++++++++++-------- modules/bedtools/complement/main.nf | 9 ++- modules/bedtools/complement/meta.yml | 2 +- modules/bedtools/genomecov/functions.nf | 58 +++++++++++-------- modules/bedtools/genomecov/main.nf | 14 +++-- modules/bedtools/genomecov/meta.yml | 2 +- modules/bedtools/getfasta/functions.nf | 58 +++++++++++-------- modules/bedtools/getfasta/main.nf | 9 ++- modules/bedtools/getfasta/meta.yml | 2 +- modules/bedtools/intersect/functions.nf | 58 +++++++++++-------- modules/bedtools/intersect/main.nf | 9 ++- modules/bedtools/intersect/meta.yml | 2 +- modules/bedtools/makewindows/functions.nf | 58 +++++++++++-------- modules/bedtools/makewindows/main.nf | 9 ++- modules/bedtools/makewindows/meta.yml | 2 +- modules/bedtools/maskfasta/functions.nf | 58 +++++++++++-------- modules/bedtools/maskfasta/main.nf | 9 ++- modules/bedtools/maskfasta/meta.yml | 2 +- modules/bedtools/merge/functions.nf | 58 +++++++++++-------- modules/bedtools/merge/main.nf | 9 ++- modules/bedtools/merge/meta.yml | 2 +- modules/bedtools/slop/functions.nf | 58 +++++++++++-------- modules/bedtools/slop/main.nf | 9 ++- modules/bedtools/slop/meta.yml | 2 +- modules/bedtools/sort/functions.nf | 58 +++++++++++-------- modules/bedtools/sort/main.nf | 9 ++- modules/bedtools/sort/meta.yml | 2 +- modules/bedtools/subtract/functions.nf | 58 +++++++++++-------- modules/bedtools/subtract/main.nf | 9 ++- modules/bedtools/subtract/meta.yml | 2 +- modules/bismark/align/functions.nf | 58 +++++++++++-------- modules/bismark/align/main.nf | 9 ++- modules/bismark/align/meta.yml | 2 +- modules/bismark/deduplicate/functions.nf | 58 +++++++++++-------- modules/bismark/deduplicate/main.nf | 9 ++- modules/bismark/deduplicate/meta.yml | 2 +- .../bismark/genomepreparation/functions.nf | 58 +++++++++++-------- modules/bismark/genomepreparation/main.nf | 9 ++- modules/bismark/genomepreparation/meta.yml | 2 +- .../bismark/methylationextractor/functions.nf | 58 +++++++++++-------- modules/bismark/methylationextractor/main.nf | 9 ++- modules/bismark/methylationextractor/meta.yml | 2 +- modules/bismark/report/functions.nf | 58 +++++++++++-------- modules/bismark/report/main.nf | 9 ++- modules/bismark/report/meta.yml | 2 +- modules/bismark/summary/functions.nf | 58 +++++++++++-------- modules/bismark/summary/main.nf | 9 ++- modules/bismark/summary/meta.yml | 2 +- modules/blast/blastn/functions.nf | 58 +++++++++++-------- modules/blast/blastn/main.nf | 9 ++- modules/blast/blastn/meta.yml | 2 +- modules/blast/makeblastdb/functions.nf | 58 +++++++++++-------- modules/blast/makeblastdb/main.nf | 9 ++- modules/blast/makeblastdb/meta.yml | 2 +- modules/bowtie/align/functions.nf | 58 +++++++++++-------- modules/bowtie/align/main.nf | 9 ++- modules/bowtie/align/meta.yml | 2 +- modules/bowtie/build/functions.nf | 58 +++++++++++-------- modules/bowtie/build/main.nf | 9 ++- modules/bowtie/build/meta.yml | 2 +- modules/bowtie2/align/functions.nf | 58 +++++++++++-------- modules/bowtie2/align/main.nf | 14 +++-- modules/bowtie2/align/meta.yml | 2 +- modules/bowtie2/build/functions.nf | 58 +++++++++++-------- modules/bowtie2/build/main.nf | 9 ++- modules/bowtie2/build/meta.yml | 2 +- modules/bwa/aln/functions.nf | 58 +++++++++++-------- modules/bwa/aln/main.nf | 14 +++-- modules/bwa/aln/meta.yml | 2 +- modules/bwa/index/functions.nf | 58 +++++++++++-------- modules/bwa/index/main.nf | 9 ++- modules/bwa/index/meta.yml | 2 +- modules/bwa/mem/functions.nf | 58 +++++++++++-------- modules/bwa/mem/main.nf | 9 ++- modules/bwa/mem/meta.yml | 2 +- modules/bwa/sampe/functions.nf | 58 +++++++++++-------- modules/bwa/sampe/main.nf | 9 ++- modules/bwa/sampe/meta.yml | 2 +- modules/bwa/samse/functions.nf | 58 +++++++++++-------- modules/bwa/samse/main.nf | 9 ++- modules/bwa/samse/meta.yml | 2 +- modules/bwamem2/index/functions.nf | 58 +++++++++++-------- modules/bwamem2/index/main.nf | 9 ++- modules/bwamem2/index/meta.yml | 2 +- modules/bwamem2/mem/functions.nf | 58 +++++++++++-------- modules/bwamem2/mem/main.nf | 9 ++- modules/bwamem2/mem/meta.yml | 2 +- modules/bwameth/align/functions.nf | 58 +++++++++++-------- modules/bwameth/align/main.nf | 9 ++- modules/bwameth/align/meta.yml | 2 +- modules/bwameth/index/functions.nf | 58 +++++++++++-------- modules/bwameth/index/main.nf | 9 ++- modules/bwameth/index/meta.yml | 2 +- modules/cat/cat/functions.nf | 58 +++++++++++-------- modules/cat/cat/main.nf | 9 ++- modules/cat/cat/meta.yml | 2 +- modules/cat/fastq/functions.nf | 58 +++++++++++-------- modules/chromap/chromap/functions.nf | 58 +++++++++++-------- modules/chromap/chromap/main.nf | 14 +++-- modules/chromap/chromap/meta.yml | 2 +- modules/chromap/index/functions.nf | 58 +++++++++++-------- modules/chromap/index/main.nf | 9 ++- modules/chromap/index/meta.yml | 2 +- modules/cnvkit/functions.nf | 58 +++++++++++-------- modules/cnvkit/main.nf | 9 ++- modules/cnvkit/meta.yml | 2 +- modules/cooler/digest/functions.nf | 58 +++++++++++-------- modules/cooler/digest/main.nf | 9 ++- modules/cooler/digest/meta.yml | 2 +- modules/cooler/dump/functions.nf | 58 +++++++++++-------- modules/cooler/dump/main.nf | 9 ++- modules/cooler/dump/meta.yml | 2 +- modules/cutadapt/functions.nf | 58 +++++++++++-------- modules/cutadapt/main.nf | 9 ++- modules/cutadapt/meta.yml | 2 +- modules/damageprofiler/functions.nf | 58 +++++++++++-------- modules/damageprofiler/main.nf | 9 ++- modules/damageprofiler/meta.yml | 2 +- modules/deeptools/computematrix/functions.nf | 58 +++++++++++-------- modules/deeptools/computematrix/main.nf | 9 ++- modules/deeptools/computematrix/meta.yml | 2 +- .../deeptools/plotfingerprint/functions.nf | 58 +++++++++++-------- modules/deeptools/plotfingerprint/main.nf | 9 ++- modules/deeptools/plotfingerprint/meta.yml | 2 +- modules/deeptools/plotheatmap/functions.nf | 58 +++++++++++-------- modules/deeptools/plotheatmap/main.nf | 9 ++- modules/deeptools/plotheatmap/meta.yml | 2 +- modules/deeptools/plotprofile/functions.nf | 58 +++++++++++-------- modules/deeptools/plotprofile/main.nf | 9 ++- modules/deeptools/plotprofile/meta.yml | 2 +- modules/delly/call/functions.nf | 58 +++++++++++-------- modules/delly/call/main.nf | 9 ++- modules/delly/call/meta.yml | 2 +- modules/diamond/blastp/functions.nf | 58 +++++++++++-------- modules/diamond/blastp/main.nf | 9 ++- modules/diamond/blastp/meta.yml | 2 +- modules/diamond/blastx/functions.nf | 58 +++++++++++-------- modules/diamond/blastx/main.nf | 9 ++- modules/diamond/blastx/meta.yml | 2 +- modules/diamond/makedb/functions.nf | 58 +++++++++++-------- modules/diamond/makedb/main.nf | 9 ++- modules/diamond/makedb/meta.yml | 2 +- modules/dragonflye/functions.nf | 58 +++++++++++-------- modules/dragonflye/main.nf | 9 ++- modules/dragonflye/meta.yml | 2 +- modules/dshbio/exportsegments/functions.nf | 58 +++++++++++-------- modules/dshbio/exportsegments/main.nf | 9 ++- modules/dshbio/exportsegments/meta.yml | 2 +- modules/dshbio/filterbed/functions.nf | 58 +++++++++++-------- modules/dshbio/filterbed/main.nf | 9 ++- modules/dshbio/filterbed/meta.yml | 2 +- modules/dshbio/filtergff3/functions.nf | 58 +++++++++++-------- modules/dshbio/filtergff3/main.nf | 9 ++- modules/dshbio/filtergff3/meta.yml | 2 +- modules/dshbio/splitbed/functions.nf | 58 +++++++++++-------- modules/dshbio/splitbed/main.nf | 9 ++- modules/dshbio/splitbed/meta.yml | 2 +- modules/dshbio/splitgff3/functions.nf | 58 +++++++++++-------- modules/dshbio/splitgff3/main.nf | 9 ++- modules/dshbio/splitgff3/meta.yml | 2 +- modules/ensemblvep/functions.nf | 58 +++++++++++-------- modules/ensemblvep/main.nf | 9 ++- modules/ensemblvep/meta.yml | 2 +- modules/expansionhunter/functions.nf | 58 +++++++++++-------- modules/expansionhunter/main.nf | 9 ++- modules/expansionhunter/meta.yml | 2 +- modules/fastani/functions.nf | 58 +++++++++++-------- modules/fastani/main.nf | 14 +++-- modules/fastani/meta.yml | 2 +- modules/fastp/functions.nf | 58 +++++++++++-------- modules/fastp/main.nf | 14 +++-- modules/fastp/meta.yml | 2 +- modules/fasttree/functions.nf | 58 +++++++++++-------- modules/fasttree/main.nf | 9 ++- modules/fasttree/meta.yml | 2 +- .../callmolecularconsensusreads/functions.nf | 58 +++++++++++-------- .../fgbio/callmolecularconsensusreads/main.nf | 9 ++- .../callmolecularconsensusreads/meta.yml | 2 +- modules/fgbio/sortbam/functions.nf | 58 +++++++++++-------- modules/fgbio/sortbam/main.nf | 9 ++- modules/fgbio/sortbam/meta.yml | 2 +- modules/flash/functions.nf | 58 +++++++++++-------- modules/flash/main.nf | 9 ++- modules/flash/meta.yml | 2 +- modules/gatk4/applybqsr/functions.nf | 58 +++++++++++-------- modules/gatk4/applybqsr/main.nf | 9 ++- modules/gatk4/applybqsr/meta.yml | 2 +- modules/gatk4/baserecalibrator/functions.nf | 58 +++++++++++-------- modules/gatk4/baserecalibrator/main.nf | 9 ++- modules/gatk4/baserecalibrator/meta.yml | 2 +- modules/gatk4/bedtointervallist/functions.nf | 58 +++++++++++-------- modules/gatk4/bedtointervallist/main.nf | 9 ++- modules/gatk4/bedtointervallist/meta.yml | 2 +- .../createsequencedictionary/functions.nf | 58 +++++++++++-------- .../gatk4/createsequencedictionary/main.nf | 9 ++- .../gatk4/createsequencedictionary/meta.yml | 2 +- modules/gatk4/fastqtosam/functions.nf | 58 +++++++++++-------- modules/gatk4/fastqtosam/main.nf | 9 ++- modules/gatk4/fastqtosam/meta.yml | 2 +- modules/gatk4/getpileupsummaries/functions.nf | 58 +++++++++++-------- modules/gatk4/getpileupsummaries/main.nf | 9 ++- modules/gatk4/getpileupsummaries/meta.yml | 2 +- modules/gatk4/haplotypecaller/functions.nf | 58 +++++++++++-------- modules/gatk4/haplotypecaller/main.nf | 9 ++- modules/gatk4/haplotypecaller/meta.yml | 2 +- modules/gatk4/intervallisttools/functions.nf | 58 +++++++++++-------- modules/gatk4/intervallisttools/main.nf | 9 ++- modules/gatk4/intervallisttools/meta.yml | 2 +- modules/gatk4/markduplicates/functions.nf | 58 +++++++++++-------- modules/gatk4/markduplicates/main.nf | 9 ++- modules/gatk4/markduplicates/meta.yml | 2 +- modules/gatk4/mergebamalignment/functions.nf | 58 +++++++++++-------- modules/gatk4/mergebamalignment/main.nf | 9 ++- modules/gatk4/mergebamalignment/meta.yml | 2 +- modules/gatk4/mergevcfs/functions.nf | 58 +++++++++++-------- modules/gatk4/mergevcfs/main.nf | 9 ++- modules/gatk4/mergevcfs/meta.yml | 2 +- modules/gatk4/mutect2/functions.nf | 58 +++++++++++-------- modules/gatk4/mutect2/main.nf | 9 ++- modules/gatk4/mutect2/meta.yml | 2 +- modules/gatk4/revertsam/functions.nf | 58 +++++++++++-------- modules/gatk4/revertsam/main.nf | 9 ++- modules/gatk4/revertsam/meta.yml | 2 +- modules/gatk4/samtofastq/functions.nf | 58 +++++++++++-------- modules/gatk4/samtofastq/main.nf | 9 ++- modules/gatk4/samtofastq/meta.yml | 2 +- modules/gatk4/splitncigarreads/functions.nf | 58 +++++++++++-------- modules/gatk4/splitncigarreads/main.nf | 9 ++- modules/gatk4/splitncigarreads/meta.yml | 2 +- modules/gatk4/variantfiltration/functions.nf | 58 +++++++++++-------- modules/gatk4/variantfiltration/main.nf | 9 ++- modules/gatk4/variantfiltration/meta.yml | 2 +- modules/genmap/index/functions.nf | 58 +++++++++++-------- modules/genmap/index/main.nf | 9 ++- modules/genmap/index/meta.yml | 2 +- modules/genmap/mappability/functions.nf | 58 +++++++++++-------- modules/genmap/mappability/main.nf | 9 ++- modules/genmap/mappability/meta.yml | 2 +- modules/gffread/functions.nf | 58 +++++++++++-------- modules/gffread/main.nf | 9 ++- modules/gffread/meta.yml | 2 +- modules/glnexus/functions.nf | 58 +++++++++++-------- modules/glnexus/main.nf | 9 ++- modules/glnexus/meta.yml | 2 +- modules/graphmap2/align/functions.nf | 58 +++++++++++-------- modules/graphmap2/align/main.nf | 9 ++- modules/graphmap2/align/meta.yml | 2 +- modules/graphmap2/index/functions.nf | 58 +++++++++++-------- modules/graphmap2/index/main.nf | 9 ++- modules/graphmap2/index/meta.yml | 2 +- modules/gubbins/functions.nf | 58 +++++++++++-------- modules/gubbins/main.nf | 9 ++- modules/gubbins/meta.yml | 2 +- modules/gunzip/functions.nf | 58 +++++++++++-------- modules/gunzip/main.nf | 9 ++- modules/gunzip/meta.yml | 2 +- modules/hifiasm/functions.nf | 58 +++++++++++-------- modules/hifiasm/main.nf | 14 +++-- modules/hifiasm/meta.yml | 2 +- modules/hisat2/align/functions.nf | 58 +++++++++++-------- modules/hisat2/align/main.nf | 14 +++-- modules/hisat2/align/meta.yml | 2 +- modules/hisat2/build/functions.nf | 58 +++++++++++-------- modules/hisat2/build/main.nf | 9 ++- modules/hisat2/build/meta.yml | 2 +- .../hisat2/extractsplicesites/functions.nf | 58 +++++++++++-------- modules/hisat2/extractsplicesites/main.nf | 9 ++- modules/hisat2/extractsplicesites/meta.yml | 2 +- modules/hmmer/hmmalign/functions.nf | 58 +++++++++++-------- modules/hmmer/hmmalign/main.nf | 9 ++- modules/hmmer/hmmalign/meta.yml | 2 +- modules/homer/annotatepeaks/functions.nf | 58 +++++++++++-------- modules/homer/annotatepeaks/main.nf | 9 ++- modules/homer/annotatepeaks/meta.yml | 2 +- modules/homer/findpeaks/functions.nf | 58 +++++++++++-------- modules/homer/findpeaks/main.nf | 9 ++- modules/homer/findpeaks/meta.yml | 2 +- modules/homer/maketagdirectory/functions.nf | 58 +++++++++++-------- modules/homer/maketagdirectory/main.nf | 9 ++- modules/homer/maketagdirectory/meta.yml | 2 +- modules/homer/makeucscfile/functions.nf | 58 +++++++++++-------- modules/homer/makeucscfile/main.nf | 9 ++- modules/homer/makeucscfile/meta.yml | 2 +- modules/iqtree/functions.nf | 58 +++++++++++-------- modules/iqtree/main.nf | 9 ++- modules/iqtree/meta.yml | 2 +- modules/ivar/consensus/functions.nf | 58 +++++++++++-------- modules/ivar/consensus/main.nf | 9 ++- modules/ivar/consensus/meta.yml | 2 +- modules/ivar/trim/functions.nf | 58 +++++++++++-------- modules/ivar/trim/main.nf | 9 ++- modules/ivar/trim/meta.yml | 2 +- modules/ivar/variants/functions.nf | 58 +++++++++++-------- modules/ivar/variants/main.nf | 9 ++- modules/ivar/variants/meta.yml | 2 +- modules/kallisto/index/functions.nf | 58 +++++++++++-------- modules/kallisto/index/main.nf | 9 ++- modules/kallisto/index/meta.yml | 2 +- modules/kallistobustools/count/functions.nf | 58 +++++++++++-------- modules/kallistobustools/count/main.nf | 9 ++- modules/kallistobustools/count/meta.yml | 2 +- modules/kallistobustools/ref/functions.nf | 58 +++++++++++-------- modules/kallistobustools/ref/main.nf | 14 +++-- modules/kallistobustools/ref/meta.yml | 2 +- modules/kleborate/functions.nf | 58 +++++++++++-------- modules/kleborate/main.nf | 9 ++- modules/kleborate/meta.yml | 2 +- modules/kraken2/kraken2/functions.nf | 58 +++++++++++-------- modules/kraken2/kraken2/main.nf | 9 ++- modules/kraken2/kraken2/meta.yml | 2 +- modules/last/dotplot/functions.nf | 58 +++++++++++-------- modules/last/dotplot/main.nf | 9 ++- modules/last/dotplot/meta.yml | 2 +- modules/last/lastal/functions.nf | 58 +++++++++++-------- modules/last/lastal/main.nf | 9 ++- modules/last/lastal/meta.yml | 2 +- modules/last/lastdb/functions.nf | 58 +++++++++++-------- modules/last/lastdb/main.nf | 9 ++- modules/last/lastdb/meta.yml | 2 +- modules/last/mafconvert/functions.nf | 58 +++++++++++-------- modules/last/mafconvert/main.nf | 9 ++- modules/last/mafconvert/meta.yml | 2 +- modules/last/mafswap/functions.nf | 58 +++++++++++-------- modules/last/mafswap/main.nf | 9 ++- modules/last/mafswap/meta.yml | 2 +- modules/last/postmask/functions.nf | 58 +++++++++++-------- modules/last/postmask/main.nf | 9 ++- modules/last/postmask/meta.yml | 2 +- modules/last/split/functions.nf | 58 +++++++++++-------- modules/last/split/main.nf | 9 ++- modules/last/split/meta.yml | 2 +- modules/last/train/functions.nf | 58 +++++++++++-------- modules/last/train/main.nf | 9 ++- modules/last/train/meta.yml | 2 +- modules/lib/functions.nf | 58 +++++++++++-------- modules/lofreq/call/functions.nf | 58 +++++++++++-------- modules/lofreq/call/main.nf | 9 ++- modules/lofreq/call/meta.yml | 2 +- modules/lofreq/callparallel/functions.nf | 58 +++++++++++-------- modules/lofreq/callparallel/main.nf | 9 ++- modules/lofreq/callparallel/meta.yml | 2 +- modules/lofreq/filter/functions.nf | 58 +++++++++++-------- modules/lofreq/filter/main.nf | 9 ++- modules/lofreq/filter/meta.yml | 2 +- modules/lofreq/indelqual/functions.nf | 58 +++++++++++-------- modules/lofreq/indelqual/main.nf | 9 ++- modules/lofreq/indelqual/meta.yml | 2 +- modules/macs2/callpeak/functions.nf | 58 +++++++++++-------- modules/macs2/callpeak/main.nf | 9 ++- modules/malt/build/functions.nf | 58 +++++++++++-------- modules/malt/build/main.nf | 9 ++- modules/malt/build/meta.yml | 2 +- modules/malt/run/functions.nf | 58 +++++++++++-------- modules/malt/run/main.nf | 9 ++- modules/malt/run/meta.yml | 2 +- modules/maltextract/functions.nf | 58 +++++++++++-------- modules/maltextract/main.nf | 9 ++- modules/maltextract/meta.yml | 2 +- modules/mash/sketch/functions.nf | 58 +++++++++++-------- modules/mash/sketch/main.nf | 9 ++- modules/metaphlan3/functions.nf | 58 +++++++++++-------- modules/metaphlan3/main.nf | 9 ++- modules/metaphlan3/meta.yml | 2 +- modules/methyldackel/extract/functions.nf | 58 +++++++++++-------- modules/methyldackel/extract/main.nf | 9 ++- modules/methyldackel/extract/meta.yml | 2 +- modules/methyldackel/mbias/functions.nf | 58 +++++++++++-------- modules/methyldackel/mbias/main.nf | 9 ++- modules/methyldackel/mbias/meta.yml | 2 +- modules/minia/functions.nf | 58 +++++++++++-------- modules/minia/main.nf | 9 ++- modules/minia/meta.yml | 2 +- modules/minimap2/align/functions.nf | 58 +++++++++++-------- modules/minimap2/align/main.nf | 9 ++- modules/minimap2/align/meta.yml | 2 +- modules/minimap2/index/functions.nf | 58 +++++++++++-------- modules/minimap2/index/main.nf | 9 ++- modules/minimap2/index/meta.yml | 2 +- modules/mosdepth/functions.nf | 58 +++++++++++-------- modules/mosdepth/main.nf | 9 ++- modules/mosdepth/meta.yml | 2 +- modules/msisensor/msi/functions.nf | 58 +++++++++++-------- modules/msisensor/msi/main.nf | 9 ++- modules/msisensor/msi/meta.yml | 2 +- modules/msisensor/scan/functions.nf | 58 +++++++++++-------- modules/msisensor/scan/main.nf | 9 ++- modules/msisensor/scan/meta.yml | 2 +- modules/muscle/functions.nf | 58 +++++++++++-------- modules/muscle/main.nf | 9 ++- modules/muscle/meta.yml | 2 +- modules/nanolyse/functions.nf | 58 +++++++++++-------- modules/nanolyse/main.nf | 9 ++- modules/nanolyse/meta.yml | 2 +- modules/nanoplot/functions.nf | 58 +++++++++++-------- modules/nanoplot/main.nf | 9 ++- modules/nanoplot/meta.yml | 2 +- modules/nextclade/functions.nf | 58 +++++++++++-------- modules/nextclade/main.nf | 9 ++- modules/nextclade/meta.yml | 2 +- modules/optitype/functions.nf | 58 +++++++++++-------- modules/optitype/main.nf | 9 ++- modules/optitype/meta.yml | 2 +- modules/pairix/functions.nf | 58 +++++++++++-------- modules/pairix/main.nf | 9 ++- modules/pairix/meta.yml | 2 +- modules/pairtools/dedup/functions.nf | 58 +++++++++++-------- modules/pairtools/dedup/main.nf | 9 ++- modules/pairtools/dedup/meta.yml | 2 +- modules/pairtools/flip/functions.nf | 58 +++++++++++-------- modules/pairtools/flip/main.nf | 9 ++- modules/pairtools/flip/meta.yml | 2 +- modules/pairtools/parse/functions.nf | 58 +++++++++++-------- modules/pairtools/parse/main.nf | 9 ++- modules/pairtools/parse/meta.yml | 2 +- modules/pairtools/restrict/functions.nf | 58 +++++++++++-------- modules/pairtools/restrict/main.nf | 9 ++- modules/pairtools/restrict/meta.yml | 2 +- modules/pairtools/select/functions.nf | 58 +++++++++++-------- modules/pairtools/select/main.nf | 9 ++- modules/pairtools/select/meta.yml | 2 +- modules/pairtools/sort/functions.nf | 58 +++++++++++-------- modules/pairtools/sort/main.nf | 9 ++- modules/pairtools/sort/meta.yml | 2 +- modules/pangolin/functions.nf | 58 +++++++++++-------- modules/pangolin/main.nf | 9 ++- modules/pangolin/meta.yml | 2 +- modules/pbccs/functions.nf | 58 +++++++++++-------- modules/pbccs/main.nf | 9 ++- modules/pbccs/meta.yml | 2 +- modules/phantompeakqualtools/functions.nf | 58 +++++++++++-------- modules/phantompeakqualtools/main.nf | 9 ++- .../collectmultiplemetrics/functions.nf | 58 +++++++++++-------- modules/picard/collectmultiplemetrics/main.nf | 9 ++- .../picard/collectmultiplemetrics/meta.yml | 2 +- modules/picard/collectwgsmetrics/functions.nf | 58 +++++++++++-------- modules/picard/collectwgsmetrics/main.nf | 9 ++- modules/picard/collectwgsmetrics/meta.yml | 2 +- modules/picard/filtersamreads/functions.nf | 58 +++++++++++-------- modules/picard/filtersamreads/main.nf | 14 +++-- modules/picard/filtersamreads/meta.yml | 2 +- modules/picard/markduplicates/functions.nf | 58 +++++++++++-------- modules/picard/markduplicates/main.nf | 9 ++- modules/picard/markduplicates/meta.yml | 2 +- modules/picard/mergesamfiles/functions.nf | 58 +++++++++++-------- modules/picard/mergesamfiles/main.nf | 14 +++-- modules/picard/mergesamfiles/meta.yml | 2 +- modules/picard/sortsam/functions.nf | 58 +++++++++++-------- modules/picard/sortsam/main.nf | 9 ++- modules/picard/sortsam/meta.yml | 2 +- modules/plasmidid/functions.nf | 58 +++++++++++-------- modules/plasmidid/main.nf | 9 ++- modules/plasmidid/meta.yml | 2 +- modules/plink/vcf/functions.nf | 58 +++++++++++-------- modules/plink/vcf/main.nf | 9 ++- modules/plink/vcf/meta.yml | 2 +- modules/preseq/lcextrap/functions.nf | 58 +++++++++++-------- modules/preseq/lcextrap/main.nf | 9 ++- modules/preseq/lcextrap/meta.yml | 2 +- modules/prodigal/functions.nf | 58 +++++++++++-------- modules/prodigal/main.nf | 9 ++- modules/prodigal/meta.yml | 2 +- modules/prokka/functions.nf | 58 +++++++++++-------- modules/prokka/main.nf | 9 ++- modules/prokka/meta.yml | 2 +- modules/pycoqc/functions.nf | 58 +++++++++++-------- modules/pycoqc/main.nf | 9 ++- modules/pycoqc/meta.yml | 2 +- modules/pydamage/analyze/functions.nf | 58 +++++++++++-------- modules/pydamage/analyze/main.nf | 9 ++- modules/pydamage/analyze/meta.yml | 2 +- modules/pydamage/filter/functions.nf | 58 +++++++++++-------- modules/pydamage/filter/main.nf | 9 ++- modules/pydamage/filter/meta.yml | 2 +- modules/qcat/functions.nf | 58 +++++++++++-------- modules/qcat/main.nf | 9 ++- modules/qcat/meta.yml | 2 +- modules/qualimap/bamqc/functions.nf | 58 +++++++++++-------- modules/qualimap/bamqc/main.nf | 9 ++- modules/qualimap/bamqc/meta.yml | 2 +- modules/qualimap/rnaseq/functions.nf | 58 +++++++++++-------- modules/qualimap/rnaseq/main.nf | 9 ++- modules/quast/functions.nf | 58 +++++++++++-------- modules/quast/main.nf | 9 ++- modules/quast/meta.yml | 2 +- modules/rapidnj/functions.nf | 58 +++++++++++-------- modules/rapidnj/main.nf | 9 ++- modules/rapidnj/meta.yml | 2 +- modules/rasusa/functions.nf | 58 +++++++++++-------- modules/rasusa/main.nf | 9 ++- modules/rasusa/meta.yml | 2 +- modules/raxmlng/functions.nf | 58 +++++++++++-------- modules/raxmlng/main.nf | 9 ++- modules/raxmlng/meta.yml | 2 +- modules/rsem/calculateexpression/functions.nf | 58 +++++++++++-------- modules/rsem/calculateexpression/main.nf | 9 ++- modules/rsem/calculateexpression/meta.yml | 2 +- modules/rsem/preparereference/functions.nf | 58 +++++++++++-------- modules/rsem/preparereference/main.nf | 14 +++-- modules/rsem/preparereference/meta.yml | 2 +- modules/rseqc/bamstat/functions.nf | 58 +++++++++++-------- modules/rseqc/bamstat/main.nf | 9 ++- modules/rseqc/bamstat/meta.yml | 2 +- modules/rseqc/inferexperiment/functions.nf | 58 +++++++++++-------- modules/rseqc/inferexperiment/main.nf | 9 ++- modules/rseqc/inferexperiment/meta.yml | 2 +- modules/rseqc/innerdistance/functions.nf | 58 +++++++++++-------- modules/rseqc/innerdistance/main.nf | 14 +++-- modules/rseqc/innerdistance/meta.yml | 2 +- modules/rseqc/junctionannotation/functions.nf | 58 +++++++++++-------- modules/rseqc/junctionannotation/main.nf | 9 ++- modules/rseqc/junctionannotation/meta.yml | 2 +- modules/rseqc/junctionsaturation/functions.nf | 58 +++++++++++-------- modules/rseqc/junctionsaturation/main.nf | 9 ++- modules/rseqc/junctionsaturation/meta.yml | 2 +- modules/rseqc/readdistribution/functions.nf | 58 +++++++++++-------- modules/rseqc/readdistribution/main.nf | 9 ++- modules/rseqc/readdistribution/meta.yml | 2 +- modules/rseqc/readduplication/functions.nf | 58 +++++++++++-------- modules/rseqc/readduplication/main.nf | 9 ++- modules/rseqc/readduplication/meta.yml | 2 +- modules/salmon/index/functions.nf | 58 +++++++++++-------- modules/salmon/index/main.nf | 9 ++- modules/salmon/index/meta.yml | 2 +- modules/salmon/quant/functions.nf | 58 +++++++++++-------- modules/salmon/quant/main.nf | 9 ++- modules/salmon/quant/meta.yml | 2 +- modules/samtools/ampliconclip/functions.nf | 58 +++++++++++-------- modules/samtools/ampliconclip/main.nf | 9 ++- modules/samtools/ampliconclip/meta.yml | 2 +- modules/samtools/faidx/functions.nf | 58 +++++++++++-------- modules/samtools/faidx/main.nf | 9 ++- modules/samtools/faidx/meta.yml | 2 +- modules/samtools/fastq/functions.nf | 58 +++++++++++-------- modules/samtools/fastq/main.nf | 9 ++- modules/samtools/fastq/meta.yml | 2 +- modules/samtools/flagstat/functions.nf | 58 +++++++++++-------- modules/samtools/flagstat/main.nf | 9 ++- modules/samtools/flagstat/meta.yml | 2 +- modules/samtools/idxstats/functions.nf | 58 +++++++++++-------- modules/samtools/idxstats/main.nf | 9 ++- modules/samtools/idxstats/meta.yml | 2 +- modules/samtools/index/functions.nf | 58 +++++++++++-------- modules/samtools/index/main.nf | 9 ++- modules/samtools/index/meta.yml | 2 +- modules/samtools/merge/functions.nf | 58 +++++++++++-------- modules/samtools/merge/main.nf | 9 ++- modules/samtools/merge/meta.yml | 2 +- modules/samtools/mpileup/functions.nf | 58 +++++++++++-------- modules/samtools/mpileup/main.nf | 9 ++- modules/samtools/mpileup/meta.yml | 2 +- modules/samtools/sort/functions.nf | 58 +++++++++++-------- modules/samtools/sort/main.nf | 9 ++- modules/samtools/sort/meta.yml | 2 +- modules/samtools/stats/functions.nf | 58 +++++++++++-------- modules/samtools/stats/main.nf | 9 ++- modules/samtools/stats/meta.yml | 2 +- modules/samtools/view/functions.nf | 58 +++++++++++-------- modules/samtools/view/main.nf | 9 ++- modules/samtools/view/meta.yml | 2 +- modules/seacr/callpeak/functions.nf | 58 +++++++++++-------- modules/seacr/callpeak/main.nf | 9 ++- modules/seacr/callpeak/meta.yml | 2 +- modules/seqkit/split2/functions.nf | 58 +++++++++++-------- modules/seqkit/split2/main.nf | 14 +++-- modules/seqkit/split2/meta.yml | 2 +- modules/seqtk/sample/functions.nf | 58 +++++++++++-------- modules/seqtk/sample/main.nf | 14 +++-- modules/seqtk/sample/meta.yml | 2 +- modules/seqtk/subseq/functions.nf | 58 +++++++++++-------- modules/seqtk/subseq/main.nf | 9 ++- modules/seqtk/subseq/meta.yml | 2 +- modules/sequenzautils/bam2seqz/functions.nf | 58 +++++++++++-------- modules/sequenzautils/bam2seqz/main.nf | 9 ++- modules/sequenzautils/bam2seqz/meta.yml | 2 +- modules/sequenzautils/gcwiggle/functions.nf | 58 +++++++++++-------- modules/sequenzautils/gcwiggle/main.nf | 9 ++- modules/sequenzautils/gcwiggle/meta.yml | 2 +- modules/seqwish/induce/functions.nf | 58 +++++++++++-------- modules/seqwish/induce/main.nf | 9 ++- modules/seqwish/induce/meta.yml | 2 +- modules/shovill/functions.nf | 58 +++++++++++-------- modules/shovill/main.nf | 9 ++- modules/shovill/meta.yml | 2 +- modules/snpdists/functions.nf | 58 +++++++++++-------- modules/snpdists/main.nf | 9 ++- modules/snpdists/meta.yml | 2 +- modules/snpeff/functions.nf | 58 +++++++++++-------- modules/snpeff/main.nf | 9 ++- modules/snpeff/meta.yml | 2 +- modules/snpsites/functions.nf | 58 +++++++++++-------- modules/snpsites/main.nf | 9 ++- modules/snpsites/meta.yml | 2 +- modules/sortmerna/functions.nf | 58 +++++++++++-------- modules/sortmerna/main.nf | 14 +++-- modules/spades/functions.nf | 58 +++++++++++-------- modules/spades/main.nf | 9 ++- modules/spades/meta.yml | 2 +- modules/staphopiasccmec/functions.nf | 58 +++++++++++-------- modules/staphopiasccmec/main.nf | 9 ++- modules/staphopiasccmec/meta.yml | 2 +- modules/star/align/functions.nf | 58 +++++++++++-------- modules/star/align/main.nf | 9 ++- modules/star/align/meta.yml | 2 +- modules/star/genomegenerate/functions.nf | 58 +++++++++++-------- modules/star/genomegenerate/main.nf | 14 +++-- modules/star/genomegenerate/meta.yml | 2 +- modules/strelka/germline/functions.nf | 58 +++++++++++-------- modules/strelka/germline/main.nf | 9 ++- modules/strelka/germline/meta.yml | 2 +- modules/stringtie/merge/functions.nf | 58 +++++++++++-------- modules/stringtie/merge/main.nf | 9 ++- modules/stringtie/stringtie/functions.nf | 58 +++++++++++-------- modules/stringtie/stringtie/main.nf | 9 ++- modules/stringtie/stringtie/meta.yml | 2 +- modules/subread/featurecounts/functions.nf | 58 +++++++++++-------- modules/subread/featurecounts/main.nf | 9 ++- modules/subread/featurecounts/meta.yml | 2 +- modules/tabix/bgzip/functions.nf | 58 +++++++++++-------- modules/tabix/bgzip/main.nf | 9 ++- modules/tabix/bgzip/meta.yml | 2 +- modules/tabix/bgziptabix/functions.nf | 58 +++++++++++-------- modules/tabix/bgziptabix/main.nf | 9 ++- modules/tabix/bgziptabix/meta.yml | 2 +- modules/tabix/tabix/functions.nf | 58 +++++++++++-------- modules/tabix/tabix/main.nf | 9 ++- modules/tabix/tabix/meta.yml | 2 +- modules/tiddit/sv/functions.nf | 58 +++++++++++-------- modules/tiddit/sv/main.nf | 9 ++- modules/tiddit/sv/meta.yml | 2 +- modules/trimgalore/functions.nf | 58 +++++++++++-------- modules/trimgalore/main.nf | 14 +++-- modules/trimgalore/meta.yml | 2 +- modules/ucsc/bed12tobigbed/functions.nf | 58 +++++++++++-------- modules/ucsc/bed12tobigbed/main.nf | 9 ++- modules/ucsc/bed12tobigbed/meta.yml | 2 +- modules/ucsc/bedclip/functions.nf | 58 +++++++++++-------- modules/ucsc/bedclip/main.nf | 9 ++- modules/ucsc/bedclip/meta.yml | 2 +- modules/ucsc/bedgraphtobigwig/functions.nf | 58 +++++++++++-------- modules/ucsc/bedgraphtobigwig/main.nf | 9 ++- modules/ucsc/bedgraphtobigwig/meta.yml | 2 +- .../ucsc/bigwigaverageoverbed/functions.nf | 58 +++++++++++-------- modules/ucsc/bigwigaverageoverbed/main.nf | 9 ++- modules/ucsc/bigwigaverageoverbed/meta.yml | 2 +- modules/ucsc/wigtobigwig/functions.nf | 58 +++++++++++-------- modules/ucsc/wigtobigwig/main.nf | 9 ++- modules/ucsc/wigtobigwig/meta.yml | 2 +- modules/umitools/dedup/functions.nf | 58 +++++++++++-------- modules/umitools/dedup/main.nf | 9 ++- modules/umitools/extract/functions.nf | 58 +++++++++++-------- modules/umitools/extract/main.nf | 14 +++-- modules/unicycler/functions.nf | 58 +++++++++++-------- modules/unicycler/main.nf | 9 ++- modules/unicycler/meta.yml | 4 +- modules/untar/functions.nf | 58 +++++++++++-------- modules/untar/main.nf | 9 ++- modules/untar/meta.yml | 2 +- modules/unzip/functions.nf | 58 +++++++++++-------- modules/unzip/main.nf | 9 ++- modules/unzip/meta.yml | 2 +- modules/variantbam/functions.nf | 58 +++++++++++-------- modules/variantbam/main.nf | 9 ++- modules/variantbam/meta.yml | 2 +- modules/vcftools/functions.nf | 58 +++++++++++-------- modules/vcftools/main.nf | 9 ++- modules/vcftools/meta.yml | 2 +- modules/yara/index/functions.nf | 58 +++++++++++-------- modules/yara/index/main.nf | 9 ++- modules/yara/index/meta.yml | 2 +- modules/yara/mapper/functions.nf | 58 +++++++++++-------- modules/yara/mapper/main.nf | 14 +++-- modules/yara/mapper/meta.yml | 2 +- 744 files changed, 10399 insertions(+), 7063 deletions(-) diff --git a/modules/abacas/functions.nf b/modules/abacas/functions.nf index da9da093..85628ee0 100644 --- a/modules/abacas/functions.nf +++ b/modules/abacas/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/abacas/main.nf b/modules/abacas/main.nf index 6ec65ea2..0e46f854 100644 --- a/modules/abacas/main.nf +++ b/modules/abacas/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process ABACAS { output: tuple val(meta), path('*.abacas*'), emit: results - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -40,6 +40,9 @@ process ABACAS { mv nucmer.filtered.delta ${prefix}.abacas.nucmer.filtered.delta mv nucmer.tiling ${prefix}.abacas.nucmer.tiling mv unused_contigs.out ${prefix}.abacas.unused.contigs.out - echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(abacas.pl -v 2>&1 | sed 's/^.*ABACAS.//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/abacas/meta.yml b/modules/abacas/meta.yml index d60afee0..d8c45628 100644 --- a/modules/abacas/meta.yml +++ b/modules/abacas/meta.yml @@ -51,7 +51,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" diff --git a/modules/adapterremoval/functions.nf b/modules/adapterremoval/functions.nf index da9da093..85628ee0 100644 --- a/modules/adapterremoval/functions.nf +++ b/modules/adapterremoval/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/adapterremoval/main.nf b/modules/adapterremoval/main.nf index 08b1b8bf..cbf0957a 100644 --- a/modules/adapterremoval/main.nf +++ b/modules/adapterremoval/main.nf @@ -1,4 +1,4 @@ -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process ADAPTERREMOVAL { output: tuple val(meta), path('*.fastq.gz'), emit: reads tuple val(meta), path('*.log') , emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,7 +41,10 @@ process ADAPTERREMOVAL { --seed 42 \\ --gzip \\ - AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g") + END_VERSIONS """ } else if (!meta.single_end && !meta.collapse) { """ @@ -57,7 +60,10 @@ process ADAPTERREMOVAL { --seed 42 \\ --gzip \\ - AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g") + END_VERSIONS """ } else { """ @@ -73,7 +79,10 @@ process ADAPTERREMOVAL { --gzip \\ cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz - AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g") + END_VERSIONS """ } diff --git a/modules/adapterremoval/meta.yml b/modules/adapterremoval/meta.yml index 15e0a201..6282436a 100644 --- a/modules/adapterremoval/meta.yml +++ b/modules/adapterremoval/meta.yml @@ -44,7 +44,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@maxibor" diff --git a/modules/agrvate/functions.nf b/modules/agrvate/functions.nf index da9da093..85628ee0 100644 --- a/modules/agrvate/functions.nf +++ b/modules/agrvate/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/agrvate/main.nf b/modules/agrvate/main.nf index 8f504927..44ec0825 100644 --- a/modules/agrvate/main.nf +++ b/modules/agrvate/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process AGRVATE { output: tuple val(meta), path("${fasta.baseName}-results/${fasta.baseName}-summary.tab"), emit: summary path "${fasta.baseName}-results" , emit: results_dir - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process AGRVATE { $options.args \\ -i $fasta - echo \$(agrvate -v 2>&1) | sed 's/agrvate //;' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(agrvate -v 2>&1 | sed 's/agrvate //;') + END_VERSIONS """ } diff --git a/modules/agrvate/meta.yml b/modules/agrvate/meta.yml index 97aa5f58..bd27050a 100644 --- a/modules/agrvate/meta.yml +++ b/modules/agrvate/meta.yml @@ -41,6 +41,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@abhi18av" diff --git a/modules/allelecounter/functions.nf b/modules/allelecounter/functions.nf index da9da093..85628ee0 100644 --- a/modules/allelecounter/functions.nf +++ b/modules/allelecounter/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/allelecounter/main.nf b/modules/allelecounter/main.nf index ad24b3c1..31ef3f79 100644 --- a/modules/allelecounter/main.nf +++ b/modules/allelecounter/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process ALLELECOUNTER { output: tuple val(meta), path("*.alleleCount"), emit: allelecount - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process ALLELECOUNTER { -b $bam \\ -o ${prefix}.alleleCount - alleleCounter --version > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(alleleCounter --version) + END_VERSIONS """ } diff --git a/modules/allelecounter/meta.yml b/modules/allelecounter/meta.yml index 28f96836..67b398f3 100644 --- a/modules/allelecounter/meta.yml +++ b/modules/allelecounter/meta.yml @@ -42,7 +42,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - alleleCount: type: file description: Allele count file diff --git a/modules/arriba/functions.nf b/modules/arriba/functions.nf index da9da093..85628ee0 100644 --- a/modules/arriba/functions.nf +++ b/modules/arriba/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/arriba/main.nf b/modules/arriba/main.nf index 739922ef..b94c22d9 100644 --- a/modules/arriba/main.nf +++ b/modules/arriba/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process ARRIBA { output: tuple val(meta), path("*.fusions.tsv") , emit: fusions tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process ARRIBA { $blacklist \\ $options.args - echo \$(arriba -h | grep 'Version:' 2>&1) | sed 's/Version:\s//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//') + END_VERSIONS """ } diff --git a/modules/arriba/meta.yml b/modules/arriba/meta.yml index 370f82ec..ddd2c75b 100644 --- a/modules/arriba/meta.yml +++ b/modules/arriba/meta.yml @@ -40,7 +40,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - fusions: type: file description: File contains fusions which pass all of Arriba's filters. diff --git a/modules/artic/guppyplex/functions.nf b/modules/artic/guppyplex/functions.nf index da9da093..85628ee0 100644 --- a/modules/artic/guppyplex/functions.nf +++ b/modules/artic/guppyplex/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/artic/guppyplex/main.nf b/modules/artic/guppyplex/main.nf index 41178298..5f91e9e3 100644 --- a/modules/artic/guppyplex/main.nf +++ b/modules/artic/guppyplex/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process ARTIC_GUPPYPLEX { output: tuple val(meta), path("*.fastq.gz"), emit: fastq - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process ARTIC_GUPPYPLEX { --output ${prefix}.fastq pigz -p $task.cpus *.fastq - echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/artic/guppyplex/meta.yml b/modules/artic/guppyplex/meta.yml index 0caaf5d2..45ec7138 100644 --- a/modules/artic/guppyplex/meta.yml +++ b/modules/artic/guppyplex/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" diff --git a/modules/artic/minion/functions.nf b/modules/artic/minion/functions.nf index da9da093..85628ee0 100644 --- a/modules/artic/minion/functions.nf +++ b/modules/artic/minion/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/artic/minion/main.nf b/modules/artic/minion/main.nf index e408551b..2f810ecf 100644 --- a/modules/artic/minion/main.nf +++ b/modules/artic/minion/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -40,7 +40,7 @@ process ARTIC_MINION { tuple val(meta), path("${prefix}.pass.vcf.gz") , emit: vcf tuple val(meta), path("${prefix}.pass.vcf.gz.tbi") , emit: tbi tuple val(meta), path("*.json"), optional:true , emit: json - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -68,6 +68,9 @@ process ARTIC_MINION { $scheme \\ $prefix - echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/artic/minion/meta.yml b/modules/artic/minion/meta.yml index 1b6a73cf..77f325e5 100644 --- a/modules/artic/minion/meta.yml +++ b/modules/artic/minion/meta.yml @@ -106,7 +106,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" diff --git a/modules/bamaligncleaner/functions.nf b/modules/bamaligncleaner/functions.nf index da9da093..85628ee0 100644 --- a/modules/bamaligncleaner/functions.nf +++ b/modules/bamaligncleaner/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bamaligncleaner/main.nf b/modules/bamaligncleaner/main.nf index 8ce73ee4..7372f274 100644 --- a/modules/bamaligncleaner/main.nf +++ b/modules/bamaligncleaner/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BAMALIGNCLEANER { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process BAMALIGNCLEANER { -o ${prefix}.bam \\ ${bam} - echo \$(bamAlignCleaner --version) | sed 's/.*version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bamAlignCleaner --version | sed 's/.*version //') + END_VERSIONS """ } diff --git a/modules/bamaligncleaner/meta.yml b/modules/bamaligncleaner/meta.yml index 8afdd44b..c236c0ea 100644 --- a/modules/bamaligncleaner/meta.yml +++ b/modules/bamaligncleaner/meta.yml @@ -30,7 +30,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: Sorted BAM/CRAM file diff --git a/modules/bandage/image/functions.nf b/modules/bandage/image/functions.nf index da9da093..85628ee0 100644 --- a/modules/bandage/image/functions.nf +++ b/modules/bandage/image/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bandage/image/main.nf b/modules/bandage/image/main.nf index 6afdb60d..c788e2e1 100644 --- a/modules/bandage/image/main.nf +++ b/modules/bandage/image/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BANDAGE_IMAGE { output: tuple val(meta), path('*.png'), emit: png tuple val(meta), path('*.svg'), emit: svg - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process BANDAGE_IMAGE { Bandage image $gfa ${prefix}.png $options.args Bandage image $gfa ${prefix}.svg $options.args - echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(Bandage --version 2>&1 | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bandage/image/meta.yml b/modules/bandage/image/meta.yml index 26c23a07..f655cae4 100644 --- a/modules/bandage/image/meta.yml +++ b/modules/bandage/image/meta.yml @@ -38,6 +38,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@heuermh" diff --git a/modules/bbmap/align/functions.nf b/modules/bbmap/align/functions.nf index da9da093..85628ee0 100644 --- a/modules/bbmap/align/functions.nf +++ b/modules/bbmap/align/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bbmap/align/main.nf b/modules/bbmap/align/main.nf index eca45ddb..8235e78d 100644 --- a/modules/bbmap/align/main.nf +++ b/modules/bbmap/align/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BBMAP_ALIGN { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -54,6 +54,9 @@ process BBMAP_ALIGN { threads=$task.cpus \\ -Xmx${task.memory.toGiga()}g - echo \$(bbversion.sh) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bbversion.sh) + END_VERSIONS """ } diff --git a/modules/bbmap/align/meta.yml b/modules/bbmap/align/meta.yml index b008ea0f..bb52f06e 100644 --- a/modules/bbmap/align/meta.yml +++ b/modules/bbmap/align/meta.yml @@ -42,7 +42,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: BAM file diff --git a/modules/bbmap/bbduk/functions.nf b/modules/bbmap/bbduk/functions.nf index da9da093..85628ee0 100644 --- a/modules/bbmap/bbduk/functions.nf +++ b/modules/bbmap/bbduk/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bbmap/bbduk/main.nf b/modules/bbmap/bbduk/main.nf index 797dc8b5..4f1540dc 100644 --- a/modules/bbmap/bbduk/main.nf +++ b/modules/bbmap/bbduk/main.nf @@ -1,4 +1,4 @@ -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BBMAP_BBDUK { output: tuple val(meta), path('*.fastq.gz'), emit: reads tuple val(meta), path('*.log') , emit: log - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process BBMAP_BBDUK { $options.args \\ $contaminants_fa \\ &> ${prefix}.bbduk.log - echo \$(bbversion.sh) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bbversion.sh) + END_VERSIONS """ } diff --git a/modules/bbmap/bbduk/meta.yml b/modules/bbmap/bbduk/meta.yml index ee2eea2c..a1ab789c 100644 --- a/modules/bbmap/bbduk/meta.yml +++ b/modules/bbmap/bbduk/meta.yml @@ -42,7 +42,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - log: type: file description: Bbduk log file diff --git a/modules/bbmap/index/functions.nf b/modules/bbmap/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/bbmap/index/functions.nf +++ b/modules/bbmap/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bbmap/index/main.nf b/modules/bbmap/index/main.nf index 0e15b13f..6f957d03 100644 --- a/modules/bbmap/index/main.nf +++ b/modules/bbmap/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BBMAP_INDEX { output: path 'ref' , emit: index - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process BBMAP_INDEX { threads=$task.cpus \\ -Xmx${task.memory.toGiga()}g - echo \$(bbversion.sh) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bbversion.sh) + END_VERSIONS """ } diff --git a/modules/bbmap/index/meta.yml b/modules/bbmap/index/meta.yml index a51a44fd..1df990b2 100644 --- a/modules/bbmap/index/meta.yml +++ b/modules/bbmap/index/meta.yml @@ -23,7 +23,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - db: type: directory description: Directory with index files diff --git a/modules/bcftools/concat/functions.nf b/modules/bcftools/concat/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/concat/functions.nf +++ b/modules/bcftools/concat/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/concat/main.nf b/modules/bcftools/concat/main.nf index 0266f4f0..fab0e83d 100644 --- a/modules/bcftools/concat/main.nf +++ b/modules/bcftools/concat/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BCFTOOLS_CONCAT { output: tuple val(meta), path("*.gz"), emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process BCFTOOLS_CONCAT { --threads $task.cpus \\ ${vcfs} - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/concat/meta.yml b/modules/bcftools/concat/meta.yml index 566e6dba..81701288 100644 --- a/modules/bcftools/concat/meta.yml +++ b/modules/bcftools/concat/meta.yml @@ -37,6 +37,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@abhi18av" diff --git a/modules/bcftools/consensus/functions.nf b/modules/bcftools/consensus/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/consensus/functions.nf +++ b/modules/bcftools/consensus/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/consensus/main.nf b/modules/bcftools/consensus/main.nf index 0403f050..29758a4b 100644 --- a/modules/bcftools/consensus/main.nf +++ b/modules/bcftools/consensus/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BCFTOOLS_CONSENSUS { output: tuple val(meta), path('*.fa'), emit: fasta - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process BCFTOOLS_CONSENSUS { header=\$(head -n 1 ${prefix}.fa | sed 's/>//g') sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/consensus/meta.yml b/modules/bcftools/consensus/meta.yml index ef14479d..4241e441 100644 --- a/modules/bcftools/consensus/meta.yml +++ b/modules/bcftools/consensus/meta.yml @@ -42,7 +42,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bcftools/filter/functions.nf b/modules/bcftools/filter/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/filter/functions.nf +++ b/modules/bcftools/filter/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/filter/main.nf b/modules/bcftools/filter/main.nf index fbdac0de..37b7e28b 100644 --- a/modules/bcftools/filter/main.nf +++ b/modules/bcftools/filter/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BCFTOOLS_FILTER { output: tuple val(meta), path("*.gz"), emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process BCFTOOLS_FILTER { $options.args \\ $vcf - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/filter/meta.yml b/modules/bcftools/filter/meta.yml index fe9a57e6..6842b1f8 100644 --- a/modules/bcftools/filter/meta.yml +++ b/modules/bcftools/filter/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bcftools/isec/functions.nf b/modules/bcftools/isec/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/isec/functions.nf +++ b/modules/bcftools/isec/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/isec/main.nf b/modules/bcftools/isec/main.nf index 28c6103e..f700f35c 100644 --- a/modules/bcftools/isec/main.nf +++ b/modules/bcftools/isec/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BCFTOOLS_ISEC { output: tuple val(meta), path("${prefix}"), emit: results - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process BCFTOOLS_ISEC { $options.args \\ -p $prefix \\ *.vcf.gz - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/isec/meta.yml b/modules/bcftools/isec/meta.yml index fb8f4b4e..7a75a3af 100644 --- a/modules/bcftools/isec/meta.yml +++ b/modules/bcftools/isec/meta.yml @@ -42,7 +42,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bcftools/merge/functions.nf b/modules/bcftools/merge/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/merge/functions.nf +++ b/modules/bcftools/merge/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/merge/main.nf b/modules/bcftools/merge/main.nf index 66c52281..7d8ab670 100644 --- a/modules/bcftools/merge/main.nf +++ b/modules/bcftools/merge/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BCFTOOLS_MERGE { output: tuple val(meta), path("*.gz"), emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process BCFTOOLS_MERGE { --output ${prefix}.vcf.gz \\ $options.args \\ *.vcf.gz - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/merge/meta.yml b/modules/bcftools/merge/meta.yml index fad7966e..262d883a 100644 --- a/modules/bcftools/merge/meta.yml +++ b/modules/bcftools/merge/meta.yml @@ -40,7 +40,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bcftools/mpileup/functions.nf b/modules/bcftools/mpileup/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/mpileup/functions.nf +++ b/modules/bcftools/mpileup/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/mpileup/main.nf b/modules/bcftools/mpileup/main.nf index de9b951f..1f6eecaa 100644 --- a/modules/bcftools/mpileup/main.nf +++ b/modules/bcftools/mpileup/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process BCFTOOLS_MPILEUP { tuple val(meta), path("*.gz") , emit: vcf tuple val(meta), path("*.tbi") , emit: tbi tuple val(meta), path("*stats.txt"), emit: stats - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process BCFTOOLS_MPILEUP { | bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3 tabix -p vcf -f ${prefix}.vcf.gz bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/mpileup/meta.yml b/modules/bcftools/mpileup/meta.yml index a15aea14..44f2b81e 100644 --- a/modules/bcftools/mpileup/meta.yml +++ b/modules/bcftools/mpileup/meta.yml @@ -46,7 +46,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bcftools/norm/functions.nf b/modules/bcftools/norm/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/norm/functions.nf +++ b/modules/bcftools/norm/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/norm/main.nf b/modules/bcftools/norm/main.nf index 5d8a7c3c..454fc1d2 100644 --- a/modules/bcftools/norm/main.nf +++ b/modules/bcftools/norm/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BCFTOOLS_NORM { output: tuple val(meta), path("*.gz") , emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process BCFTOOLS_NORM { --threads $task.cpus \\ ${vcf} - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/norm/meta.yml b/modules/bcftools/norm/meta.yml index abeb8904..f2534452 100644 --- a/modules/bcftools/norm/meta.yml +++ b/modules/bcftools/norm/meta.yml @@ -40,6 +40,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@abhi18av" diff --git a/modules/bcftools/query/functions.nf b/modules/bcftools/query/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/query/functions.nf +++ b/modules/bcftools/query/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/query/main.nf b/modules/bcftools/query/main.nf index 26eeca63..4815ae90 100644 --- a/modules/bcftools/query/main.nf +++ b/modules/bcftools/query/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process BCFTOOLS_QUERY { output: tuple val(meta), path("*.gz") , emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -44,6 +44,9 @@ process BCFTOOLS_QUERY { $options.args \\ ${vcf} - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/query/meta.yml b/modules/bcftools/query/meta.yml index 7806c7db..57570c64 100644 --- a/modules/bcftools/query/meta.yml +++ b/modules/bcftools/query/meta.yml @@ -56,6 +56,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@abhi18av" diff --git a/modules/bcftools/reheader/functions.nf b/modules/bcftools/reheader/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/reheader/functions.nf +++ b/modules/bcftools/reheader/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/reheader/main.nf b/modules/bcftools/reheader/main.nf index 53b00411..a949b6e9 100644 --- a/modules/bcftools/reheader/main.nf +++ b/modules/bcftools/reheader/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process BCFTOOLS_REHEADER { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process BCFTOOLS_REHEADER { -o ${prefix}.vcf.gz \\ $vcf - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/reheader/meta.yml b/modules/bcftools/reheader/meta.yml index 1b9c1a8b..823e3279 100644 --- a/modules/bcftools/reheader/meta.yml +++ b/modules/bcftools/reheader/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - vcf: type: file description: VCF with updated header diff --git a/modules/bcftools/stats/functions.nf b/modules/bcftools/stats/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/stats/functions.nf +++ b/modules/bcftools/stats/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/stats/main.nf b/modules/bcftools/stats/main.nf index 90be5d2b..f5b1f6b1 100644 --- a/modules/bcftools/stats/main.nf +++ b/modules/bcftools/stats/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process BCFTOOLS_STATS { output: tuple val(meta), path("*stats.txt"), emit: stats - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bcftools stats $options.args $vcf > ${prefix}.bcftools_stats.txt - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/stats/meta.yml b/modules/bcftools/stats/meta.yml index 6b70f83a..33675cb9 100644 --- a/modules/bcftools/stats/meta.yml +++ b/modules/bcftools/stats/meta.yml @@ -35,7 +35,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bcftools/view/functions.nf b/modules/bcftools/view/functions.nf index da9da093..85628ee0 100644 --- a/modules/bcftools/view/functions.nf +++ b/modules/bcftools/view/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bcftools/view/main.nf b/modules/bcftools/view/main.nf index 92f7036b..5a944e89 100644 --- a/modules/bcftools/view/main.nf +++ b/modules/bcftools/view/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process BCFTOOLS_VIEW { output: tuple val(meta), path("*.gz") , emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -46,6 +46,9 @@ process BCFTOOLS_VIEW { --threads $task.cpus \\ ${vcf} - echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bcftools/view/meta.yml b/modules/bcftools/view/meta.yml index 947e2562..e37e41b5 100644 --- a/modules/bcftools/view/meta.yml +++ b/modules/bcftools/view/meta.yml @@ -57,6 +57,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@abhi18av" diff --git a/modules/bedtools/bamtobed/functions.nf b/modules/bedtools/bamtobed/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/bamtobed/functions.nf +++ b/modules/bedtools/bamtobed/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/bamtobed/main.nf b/modules/bedtools/bamtobed/main.nf index 22f5713c..19986371 100644 --- a/modules/bedtools/bamtobed/main.nf +++ b/modules/bedtools/bamtobed/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BEDTOOLS_BAMTOBED { output: tuple val(meta), path("*.bed"), emit: bed - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process BEDTOOLS_BAMTOBED { -i $bam \\ | bedtools sort > ${prefix}.bed - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/bamtobed/meta.yml b/modules/bedtools/bamtobed/meta.yml index 3594d2d4..5d7889ea 100644 --- a/modules/bedtools/bamtobed/meta.yml +++ b/modules/bedtools/bamtobed/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/bedtools/complement/functions.nf b/modules/bedtools/complement/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/complement/functions.nf +++ b/modules/bedtools/complement/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/complement/main.nf b/modules/bedtools/complement/main.nf index 3c39f289..5b3bbea9 100644 --- a/modules/bedtools/complement/main.nf +++ b/modules/bedtools/complement/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BEDTOOLS_COMPLEMENT { output: tuple val(meta), path('*.bed'), emit: bed - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process BEDTOOLS_COMPLEMENT { $options.args \\ > ${prefix}.bed - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/complement/meta.yml b/modules/bedtools/complement/meta.yml index 60d97263..183c9e8f 100644 --- a/modules/bedtools/complement/meta.yml +++ b/modules/bedtools/complement/meta.yml @@ -35,7 +35,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@Emiller88" - "@sruthipsuresh" diff --git a/modules/bedtools/genomecov/functions.nf b/modules/bedtools/genomecov/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/genomecov/functions.nf +++ b/modules/bedtools/genomecov/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/genomecov/main.nf b/modules/bedtools/genomecov/main.nf index f9b87464..b5deedf1 100644 --- a/modules/bedtools/genomecov/main.nf +++ b/modules/bedtools/genomecov/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process BEDTOOLS_GENOMECOV { output: tuple val(meta), path("*.${extension}"), emit: genomecov - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -38,7 +38,10 @@ process BEDTOOLS_GENOMECOV { $options.args \\ > ${prefix}.${extension} - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } else { """ @@ -49,7 +52,10 @@ process BEDTOOLS_GENOMECOV { $options.args \\ > ${prefix}.${extension} - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } } diff --git a/modules/bedtools/genomecov/meta.yml b/modules/bedtools/genomecov/meta.yml index f629665c..7f28c185 100644 --- a/modules/bedtools/genomecov/meta.yml +++ b/modules/bedtools/genomecov/meta.yml @@ -38,7 +38,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@Emiller88" - "@sruthipsuresh" diff --git a/modules/bedtools/getfasta/functions.nf b/modules/bedtools/getfasta/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/getfasta/functions.nf +++ b/modules/bedtools/getfasta/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/getfasta/main.nf b/modules/bedtools/getfasta/main.nf index 374a310b..72e457dc 100644 --- a/modules/bedtools/getfasta/main.nf +++ b/modules/bedtools/getfasta/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BEDTOOLS_GETFASTA { output: path "*.fa" , emit: fasta - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process BEDTOOLS_GETFASTA { -bed $bed \\ -fo ${prefix}.fa - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/getfasta/meta.yml b/modules/bedtools/getfasta/meta.yml index 1ca63bdc..1ddd4bbb 100644 --- a/modules/bedtools/getfasta/meta.yml +++ b/modules/bedtools/getfasta/meta.yml @@ -27,7 +27,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bedtools/intersect/functions.nf b/modules/bedtools/intersect/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/intersect/functions.nf +++ b/modules/bedtools/intersect/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/intersect/main.nf b/modules/bedtools/intersect/main.nf index 4519783a..b75bd116 100644 --- a/modules/bedtools/intersect/main.nf +++ b/modules/bedtools/intersect/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BEDTOOLS_INTERSECT { output: tuple val(meta), path("*.${extension}"), emit: intersect - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process BEDTOOLS_INTERSECT { $options.args \\ > ${prefix}.${extension} - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/intersect/meta.yml b/modules/bedtools/intersect/meta.yml index e944e355..2c229884 100644 --- a/modules/bedtools/intersect/meta.yml +++ b/modules/bedtools/intersect/meta.yml @@ -38,7 +38,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@Emiller88" - "@sruthipsuresh" diff --git a/modules/bedtools/makewindows/functions.nf b/modules/bedtools/makewindows/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/makewindows/functions.nf +++ b/modules/bedtools/makewindows/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/makewindows/main.nf b/modules/bedtools/makewindows/main.nf index d3e82f86..5e93f0ae 100644 --- a/modules/bedtools/makewindows/main.nf +++ b/modules/bedtools/makewindows/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BEDTOOLS_MAKEWINDOWS { output: tuple val(meta), path("*.tab"), emit: tab - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process BEDTOOLS_MAKEWINDOWS { $options.args \\ > ${prefix}.tab - echo \$(bedtools --version) | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/makewindows/meta.yml b/modules/bedtools/makewindows/meta.yml index 3c1378b8..dcddbc75 100644 --- a/modules/bedtools/makewindows/meta.yml +++ b/modules/bedtools/makewindows/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - tab: type: file description: Windows TAB file (BED or BED-like format) diff --git a/modules/bedtools/maskfasta/functions.nf b/modules/bedtools/maskfasta/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/maskfasta/functions.nf +++ b/modules/bedtools/maskfasta/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/maskfasta/main.nf b/modules/bedtools/maskfasta/main.nf index 02110149..67097f3f 100644 --- a/modules/bedtools/maskfasta/main.nf +++ b/modules/bedtools/maskfasta/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BEDTOOLS_MASKFASTA { output: tuple val(meta), path("*.fa"), emit: fasta - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process BEDTOOLS_MASKFASTA { -fi $fasta \\ -bed $bed \\ -fo ${prefix}.fa - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/maskfasta/meta.yml b/modules/bedtools/maskfasta/meta.yml index b6e494e6..0474118b 100644 --- a/modules/bedtools/maskfasta/meta.yml +++ b/modules/bedtools/maskfasta/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bedtools/merge/functions.nf b/modules/bedtools/merge/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/merge/functions.nf +++ b/modules/bedtools/merge/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/merge/main.nf b/modules/bedtools/merge/main.nf index 4ac7d1a5..ba8348af 100644 --- a/modules/bedtools/merge/main.nf +++ b/modules/bedtools/merge/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BEDTOOLS_MERGE { output: tuple val(meta), path('*.bed'), emit: bed - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process BEDTOOLS_MERGE { $options.args \\ > ${prefix}.bed - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/merge/meta.yml b/modules/bedtools/merge/meta.yml index f75bea67..0618c0ff 100644 --- a/modules/bedtools/merge/meta.yml +++ b/modules/bedtools/merge/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@Emiller88" - "@sruthipsuresh" diff --git a/modules/bedtools/slop/functions.nf b/modules/bedtools/slop/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/slop/functions.nf +++ b/modules/bedtools/slop/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/slop/main.nf b/modules/bedtools/slop/main.nf index 33dc1930..6644b8db 100644 --- a/modules/bedtools/slop/main.nf +++ b/modules/bedtools/slop/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BEDTOOLS_SLOP { output: tuple val(meta), path("*.bed"), emit: bed - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,7 +37,10 @@ process BEDTOOLS_SLOP { $options.args \\ > ${prefix}.bed - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/slop/meta.yml b/modules/bedtools/slop/meta.yml index 3d4e2091..bdcdc1d2 100644 --- a/modules/bedtools/slop/meta.yml +++ b/modules/bedtools/slop/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@Emiller88" - "@sruthipsuresh" diff --git a/modules/bedtools/sort/functions.nf b/modules/bedtools/sort/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/sort/functions.nf +++ b/modules/bedtools/sort/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/sort/main.nf b/modules/bedtools/sort/main.nf index 908514d9..acc4a593 100644 --- a/modules/bedtools/sort/main.nf +++ b/modules/bedtools/sort/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BEDTOOLS_SORT { output: tuple val(meta), path('*.bed'), emit: bed - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process BEDTOOLS_SORT { $options.args \\ > ${prefix}.bed - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/sort/meta.yml b/modules/bedtools/sort/meta.yml index 9962a4f2..d09886a5 100644 --- a/modules/bedtools/sort/meta.yml +++ b/modules/bedtools/sort/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@Emiller88" - "@sruthipsuresh" diff --git a/modules/bedtools/subtract/functions.nf b/modules/bedtools/subtract/functions.nf index da9da093..85628ee0 100644 --- a/modules/bedtools/subtract/functions.nf +++ b/modules/bedtools/subtract/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bedtools/subtract/main.nf b/modules/bedtools/subtract/main.nf index 5780cd65..a8e2ad02 100644 --- a/modules/bedtools/subtract/main.nf +++ b/modules/bedtools/subtract/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BEDTOOLS_SUBTRACT { output: tuple val(meta), path("*.bed"), emit: bed - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process BEDTOOLS_SUBTRACT { $options.args \\ > ${prefix}.bed - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS """ } diff --git a/modules/bedtools/subtract/meta.yml b/modules/bedtools/subtract/meta.yml index a1a1e087..8c99b80a 100644 --- a/modules/bedtools/subtract/meta.yml +++ b/modules/bedtools/subtract/meta.yml @@ -39,7 +39,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@sidorov-si" diff --git a/modules/bismark/align/functions.nf b/modules/bismark/align/functions.nf index da9da093..85628ee0 100644 --- a/modules/bismark/align/functions.nf +++ b/modules/bismark/align/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bismark/align/main.nf b/modules/bismark/align/main.nf index 02f439f6..00510272 100644 --- a/modules/bismark/align/main.nf +++ b/modules/bismark/align/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process BISMARK_ALIGN { tuple val(meta), path("*bam") , emit: bam tuple val(meta), path("*report.txt"), emit: report tuple val(meta), path("*fq.gz") , optional:true, emit: unmapped - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process BISMARK_ALIGN { --genome $index \\ --bam - echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS """ } diff --git a/modules/bismark/align/meta.yml b/modules/bismark/align/meta.yml index ed3b1999..d9bacf04 100644 --- a/modules/bismark/align/meta.yml +++ b/modules/bismark/align/meta.yml @@ -53,6 +53,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/bismark/deduplicate/functions.nf b/modules/bismark/deduplicate/functions.nf index da9da093..85628ee0 100644 --- a/modules/bismark/deduplicate/functions.nf +++ b/modules/bismark/deduplicate/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bismark/deduplicate/main.nf b/modules/bismark/deduplicate/main.nf index 6d7010af..6e3219f0 100644 --- a/modules/bismark/deduplicate/main.nf +++ b/modules/bismark/deduplicate/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BISMARK_DEDUPLICATE { output: tuple val(meta), path("*.deduplicated.bam") , emit: bam tuple val(meta), path("*.deduplication_report.txt"), emit: report - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process BISMARK_DEDUPLICATE { $seqtype \\ --bam $bam - echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS """ } diff --git a/modules/bismark/deduplicate/meta.yml b/modules/bismark/deduplicate/meta.yml index 117eed49..11d8797b 100644 --- a/modules/bismark/deduplicate/meta.yml +++ b/modules/bismark/deduplicate/meta.yml @@ -46,6 +46,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/bismark/genomepreparation/functions.nf b/modules/bismark/genomepreparation/functions.nf index da9da093..85628ee0 100644 --- a/modules/bismark/genomepreparation/functions.nf +++ b/modules/bismark/genomepreparation/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bismark/genomepreparation/main.nf b/modules/bismark/genomepreparation/main.nf index 3d48d955..029804d9 100644 --- a/modules/bismark/genomepreparation/main.nf +++ b/modules/bismark/genomepreparation/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BISMARK_GENOMEPREPARATION { output: path "BismarkIndex" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -32,6 +32,9 @@ process BISMARK_GENOMEPREPARATION { $options.args \\ BismarkIndex - echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS """ } diff --git a/modules/bismark/genomepreparation/meta.yml b/modules/bismark/genomepreparation/meta.yml index a31add8a..6d267343 100644 --- a/modules/bismark/genomepreparation/meta.yml +++ b/modules/bismark/genomepreparation/meta.yml @@ -31,6 +31,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/bismark/methylationextractor/functions.nf b/modules/bismark/methylationextractor/functions.nf index da9da093..85628ee0 100644 --- a/modules/bismark/methylationextractor/functions.nf +++ b/modules/bismark/methylationextractor/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bismark/methylationextractor/main.nf b/modules/bismark/methylationextractor/main.nf index cdc4999c..5968d38f 100644 --- a/modules/bismark/methylationextractor/main.nf +++ b/modules/bismark/methylationextractor/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -28,7 +28,7 @@ process BISMARK_METHYLATIONEXTRACTOR { tuple val(meta), path("*.cov.gz") , emit: coverage tuple val(meta), path("*_splitting_report.txt"), emit: report tuple val(meta), path("*.M-bias.txt") , emit: mbias - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def seqtype = meta.single_end ? '-s' : '-p' @@ -43,6 +43,9 @@ process BISMARK_METHYLATIONEXTRACTOR { $options.args \\ $bam - echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS """ } diff --git a/modules/bismark/methylationextractor/meta.yml b/modules/bismark/methylationextractor/meta.yml index a201b586..2ae7cf64 100644 --- a/modules/bismark/methylationextractor/meta.yml +++ b/modules/bismark/methylationextractor/meta.yml @@ -61,6 +61,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/bismark/report/functions.nf b/modules/bismark/report/functions.nf index da9da093..85628ee0 100644 --- a/modules/bismark/report/functions.nf +++ b/modules/bismark/report/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bismark/report/main.nf b/modules/bismark/report/main.nf index 180efc7e..8148b061 100644 --- a/modules/bismark/report/main.nf +++ b/modules/bismark/report/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process BISMARK_REPORT { output: tuple val(meta), path("*report.{html,txt}"), emit: report - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ bismark2report $options.args - echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS """ } diff --git a/modules/bismark/report/meta.yml b/modules/bismark/report/meta.yml index 3e8da1d0..57b8c746 100644 --- a/modules/bismark/report/meta.yml +++ b/modules/bismark/report/meta.yml @@ -54,6 +54,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/bismark/summary/functions.nf b/modules/bismark/summary/functions.nf index da9da093..85628ee0 100644 --- a/modules/bismark/summary/functions.nf +++ b/modules/bismark/summary/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bismark/summary/main.nf b/modules/bismark/summary/main.nf index f5c03529..ae8ac27c 100644 --- a/modules/bismark/summary/main.nf +++ b/modules/bismark/summary/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,13 +26,16 @@ process BISMARK_SUMMARY { output: path "*report.{html,txt}", emit: summary - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ bismark2summary - echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS """ } diff --git a/modules/bismark/summary/meta.yml b/modules/bismark/summary/meta.yml index a88bf8f6..37d8951b 100644 --- a/modules/bismark/summary/meta.yml +++ b/modules/bismark/summary/meta.yml @@ -48,6 +48,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/blast/blastn/functions.nf b/modules/blast/blastn/functions.nf index da9da093..85628ee0 100644 --- a/modules/blast/blastn/functions.nf +++ b/modules/blast/blastn/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/blast/blastn/main.nf b/modules/blast/blastn/main.nf index 87e012e2..1146ede4 100644 --- a/modules/blast/blastn/main.nf +++ b/modules/blast/blastn/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BLAST_BLASTN { output: tuple val(meta), path('*.blastn.txt'), emit: txt - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process BLAST_BLASTN { -query $fasta \\ $options.args \\ -out ${prefix}.blastn.txt - echo \$(blastn -version 2>&1) | sed 's/^.*blastn: //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/blast/blastn/meta.yml b/modules/blast/blastn/meta.yml index d04889a8..b4a832ea 100644 --- a/modules/blast/blastn/meta.yml +++ b/modules/blast/blastn/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/blast/makeblastdb/functions.nf b/modules/blast/makeblastdb/functions.nf index da9da093..85628ee0 100644 --- a/modules/blast/makeblastdb/functions.nf +++ b/modules/blast/makeblastdb/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/blast/makeblastdb/main.nf b/modules/blast/makeblastdb/main.nf index c938e8f6..9ee02108 100644 --- a/modules/blast/makeblastdb/main.nf +++ b/modules/blast/makeblastdb/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process BLAST_MAKEBLASTDB { output: path 'blast_db' , emit: db - path '*.version.txt', emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process BLAST_MAKEBLASTDB { $options.args mkdir blast_db mv ${fasta}* blast_db - echo \$(blastn -version 2>&1) | sed 's/^.*blastn: //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/blast/makeblastdb/meta.yml b/modules/blast/makeblastdb/meta.yml index 0ea4903f..9a5957db 100644 --- a/modules/blast/makeblastdb/meta.yml +++ b/modules/blast/makeblastdb/meta.yml @@ -24,7 +24,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bowtie/align/functions.nf b/modules/bowtie/align/functions.nf index da9da093..85628ee0 100644 --- a/modules/bowtie/align/functions.nf +++ b/modules/bowtie/align/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bowtie/align/main.nf b/modules/bowtie/align/main.nf index 9cafbfd2..3357a592 100644 --- a/modules/bowtie/align/main.nf +++ b/modules/bowtie/align/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process BOWTIE_ALIGN { output: tuple val(meta), path('*.bam'), emit: bam tuple val(meta), path('*.out'), emit: log - path '*.version.txt' , emit: version + path "versions.yml" , emit: version tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq script: @@ -55,6 +55,9 @@ process BOWTIE_ALIGN { gzip ${prefix}.unmapped_2.fastq fi - echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bowtie --version 2>&1 | sed 's/^.*bowtie-align-s version //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bowtie/align/meta.yml b/modules/bowtie/align/meta.yml index bea8b4dd..e5ada585 100644 --- a/modules/bowtie/align/meta.yml +++ b/modules/bowtie/align/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - fastq: type: file description: Unaligned FastQ files diff --git a/modules/bowtie/build/functions.nf b/modules/bowtie/build/functions.nf index da9da093..85628ee0 100644 --- a/modules/bowtie/build/functions.nf +++ b/modules/bowtie/build/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bowtie/build/main.nf b/modules/bowtie/build/main.nf index 3a6071a9..382e6717 100644 --- a/modules/bowtie/build/main.nf +++ b/modules/bowtie/build/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process BOWTIE_BUILD { output: path 'bowtie' , emit: index - path '*.version.txt', emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ mkdir bowtie bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName} - echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bowtie --version 2>&1 | sed 's/^.*bowtie-align-s version //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bowtie/build/meta.yml b/modules/bowtie/build/meta.yml index a2da42c6..e97068f6 100644 --- a/modules/bowtie/build/meta.yml +++ b/modules/bowtie/build/meta.yml @@ -25,7 +25,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/bowtie2/align/functions.nf b/modules/bowtie2/align/functions.nf index da9da093..85628ee0 100644 --- a/modules/bowtie2/align/functions.nf +++ b/modules/bowtie2/align/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf index d43d479d..e1657a8f 100644 --- a/modules/bowtie2/align/main.nf +++ b/modules/bowtie2/align/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process BOWTIE2_ALIGN { output: tuple val(meta), path('*.bam'), emit: bam tuple val(meta), path('*.log'), emit: log - path '*.version.txt' , emit: version + path "versions.yml" , emit: version tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq script: @@ -45,7 +45,10 @@ process BOWTIE2_ALIGN { 2> ${prefix}.bowtie2.log \\ | samtools view -@ ${split_cpus} $options.args2 -bhS -o ${prefix}.bam - - echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bowtie2 --version 2>&1 | sed 's/^.*bowtie2-align-s version //; s/ .*\$//') + END_VERSIONS """ } else { def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' @@ -67,7 +70,10 @@ process BOWTIE2_ALIGN { if [ -f ${prefix}.unmapped.fastq.2.gz ]; then mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz fi - echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bowtie2 --version 2>&1 | sed 's/^.*bowtie2-align-s version //; s/ .*\$//') + END_VERSIONS """ } } diff --git a/modules/bowtie2/align/meta.yml b/modules/bowtie2/align/meta.yml index 9d9cd004..cba6eacf 100644 --- a/modules/bowtie2/align/meta.yml +++ b/modules/bowtie2/align/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - fastq: type: file description: Unaligned FastQ files diff --git a/modules/bowtie2/build/functions.nf b/modules/bowtie2/build/functions.nf index da9da093..85628ee0 100644 --- a/modules/bowtie2/build/functions.nf +++ b/modules/bowtie2/build/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bowtie2/build/main.nf b/modules/bowtie2/build/main.nf index 442fed18..04880aeb 100644 --- a/modules/bowtie2/build/main.nf +++ b/modules/bowtie2/build/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process BOWTIE2_BUILD { output: path 'bowtie2' , emit: index - path '*.version.txt', emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ mkdir bowtie2 bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName} - echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bowtie2 --version 2>&1 | sed 's/^.*bowtie2-align-s version //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/bowtie2/build/meta.yml b/modules/bowtie2/build/meta.yml index 0a4cd3de..70045f3c 100644 --- a/modules/bowtie2/build/meta.yml +++ b/modules/bowtie2/build/meta.yml @@ -26,7 +26,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/bwa/aln/functions.nf b/modules/bwa/aln/functions.nf index da9da093..85628ee0 100644 --- a/modules/bwa/aln/functions.nf +++ b/modules/bwa/aln/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bwa/aln/main.nf b/modules/bwa/aln/main.nf index 59f1396c..8728884c 100644 --- a/modules/bwa/aln/main.nf +++ b/modules/bwa/aln/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BWA_ALN { output: tuple val(meta), path("*.sai"), emit: sai - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,7 +41,10 @@ process BWA_ALN { \$INDEX \\ ${reads} - echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//') + END_VERSIONS """ } else { """ @@ -61,7 +64,10 @@ process BWA_ALN { \$INDEX \\ ${reads[1]} - echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//') + END_VERSIONS """ } } diff --git a/modules/bwa/aln/meta.yml b/modules/bwa/aln/meta.yml index 4f81588d..b3797eac 100644 --- a/modules/bwa/aln/meta.yml +++ b/modules/bwa/aln/meta.yml @@ -44,7 +44,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - sai: type: file description: Single or paired SA coordinate files diff --git a/modules/bwa/index/functions.nf b/modules/bwa/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/bwa/index/functions.nf +++ b/modules/bwa/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bwa/index/main.nf b/modules/bwa/index/main.nf index aabd187c..9b64bd37 100644 --- a/modules/bwa/index/main.nf +++ b/modules/bwa/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process BWA_INDEX { output: path "bwa" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ mkdir bwa bwa index $options.args $fasta -p bwa/${fasta.baseName} - echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//') + END_VERSIONS """ } diff --git a/modules/bwa/index/meta.yml b/modules/bwa/index/meta.yml index 181204c3..43ffd73d 100644 --- a/modules/bwa/index/meta.yml +++ b/modules/bwa/index/meta.yml @@ -25,7 +25,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@maxulysse" diff --git a/modules/bwa/mem/functions.nf b/modules/bwa/mem/functions.nf index da9da093..85628ee0 100644 --- a/modules/bwa/mem/functions.nf +++ b/modules/bwa/mem/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bwa/mem/main.nf b/modules/bwa/mem/main.nf index 5e139d5a..b9096cb8 100644 --- a/modules/bwa/mem/main.nf +++ b/modules/bwa/mem/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BWA_MEM { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def split_cpus = Math.floor(task.cpus/2) @@ -42,6 +42,9 @@ process BWA_MEM { $reads \\ | samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam - - echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//') + END_VERSIONS """ } diff --git a/modules/bwa/mem/meta.yml b/modules/bwa/mem/meta.yml index 693c5450..618f20d5 100644 --- a/modules/bwa/mem/meta.yml +++ b/modules/bwa/mem/meta.yml @@ -39,7 +39,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@jeremy1805" diff --git a/modules/bwa/sampe/functions.nf b/modules/bwa/sampe/functions.nf index da9da093..85628ee0 100644 --- a/modules/bwa/sampe/functions.nf +++ b/modules/bwa/sampe/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bwa/sampe/main.nf b/modules/bwa/sampe/main.nf index 7a724908..cb3493c8 100644 --- a/modules/bwa/sampe/main.nf +++ b/modules/bwa/sampe/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BWA_SAMPE { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,6 +41,9 @@ process BWA_SAMPE { $sai \\ $reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${prefix}.bam - echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//') + END_VERSIONS """ } diff --git a/modules/bwa/sampe/meta.yml b/modules/bwa/sampe/meta.yml index 6dc1bcc5..aeb592f7 100644 --- a/modules/bwa/sampe/meta.yml +++ b/modules/bwa/sampe/meta.yml @@ -48,7 +48,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: BAM file diff --git a/modules/bwa/samse/functions.nf b/modules/bwa/samse/functions.nf index da9da093..85628ee0 100644 --- a/modules/bwa/samse/functions.nf +++ b/modules/bwa/samse/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bwa/samse/main.nf b/modules/bwa/samse/main.nf index 3fe8bdd8..82d23854 100644 --- a/modules/bwa/samse/main.nf +++ b/modules/bwa/samse/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BWA_SAMSE { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,6 +41,9 @@ process BWA_SAMSE { $sai \\ $reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${prefix}.bam - echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//') + END_VERSIONS """ } diff --git a/modules/bwa/samse/meta.yml b/modules/bwa/samse/meta.yml index 89917703..3c44741d 100644 --- a/modules/bwa/samse/meta.yml +++ b/modules/bwa/samse/meta.yml @@ -49,7 +49,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: BAM file diff --git a/modules/bwamem2/index/functions.nf b/modules/bwamem2/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/bwamem2/index/functions.nf +++ b/modules/bwamem2/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bwamem2/index/main.nf b/modules/bwamem2/index/main.nf index b667f266..f052d172 100644 --- a/modules/bwamem2/index/main.nf +++ b/modules/bwamem2/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process BWAMEM2_INDEX { output: path "bwamem2" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ mkdir bwamem2 bwa-mem2 index $options.args $fasta -p bwamem2/${fasta} - echo \$(bwa-mem2 version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwa-mem2 version 2>&1) + END_VERSIONS """ } diff --git a/modules/bwamem2/index/meta.yml b/modules/bwamem2/index/meta.yml index 9d717f73..ee84ccfc 100644 --- a/modules/bwamem2/index/meta.yml +++ b/modules/bwamem2/index/meta.yml @@ -24,6 +24,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@maxulysse" diff --git a/modules/bwamem2/mem/functions.nf b/modules/bwamem2/mem/functions.nf index da9da093..85628ee0 100644 --- a/modules/bwamem2/mem/functions.nf +++ b/modules/bwamem2/mem/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf index 5d0ff617..2838cdda 100644 --- a/modules/bwamem2/mem/main.nf +++ b/modules/bwamem2/mem/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BWAMEM2_MEM { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def split_cpus = Math.floor(task.cpus/2) @@ -42,6 +42,9 @@ process BWAMEM2_MEM { $reads \\ | samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam - - echo \$(bwa-mem2 version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwa-mem2 version 2>&1) + END_VERSIONS """ } diff --git a/modules/bwamem2/mem/meta.yml b/modules/bwamem2/mem/meta.yml index 2fc7713d..434fc7ca 100644 --- a/modules/bwamem2/mem/meta.yml +++ b/modules/bwamem2/mem/meta.yml @@ -39,6 +39,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@maxulysse" diff --git a/modules/bwameth/align/functions.nf b/modules/bwameth/align/functions.nf index da9da093..85628ee0 100644 --- a/modules/bwameth/align/functions.nf +++ b/modules/bwameth/align/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bwameth/align/main.nf b/modules/bwameth/align/main.nf index 0e8db58f..0f605bd1 100644 --- a/modules/bwameth/align/main.nf +++ b/modules/bwameth/align/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process BWAMETH_ALIGN { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def split_cpus = Math.floor(task.cpus/2) @@ -42,6 +42,9 @@ process BWAMETH_ALIGN { $reads \\ | samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam - - echo \$(bwameth.py --version 2>&1) | cut -f2 -d" " > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwameth.py --version 2>&1 | cut -f2 -d" ") + END_VERSIONS """ } diff --git a/modules/bwameth/align/meta.yml b/modules/bwameth/align/meta.yml index ac578031..03bd66f7 100644 --- a/modules/bwameth/align/meta.yml +++ b/modules/bwameth/align/meta.yml @@ -46,6 +46,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/bwameth/index/functions.nf b/modules/bwameth/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/bwameth/index/functions.nf +++ b/modules/bwameth/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/bwameth/index/main.nf b/modules/bwameth/index/main.nf index dbea0ae4..7b75d328 100644 --- a/modules/bwameth/index/main.nf +++ b/modules/bwameth/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process BWAMETH_INDEX { output: path "bwameth" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ bwameth.py index $fasta - echo \$(bwameth.py --version 2>&1) | cut -f2 -d" " > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bwameth.py --version 2>&1 | cut -f2 -d" ") + END_VERSIONS """ } diff --git a/modules/bwameth/index/meta.yml b/modules/bwameth/index/meta.yml index 79c54862..b07dbde5 100644 --- a/modules/bwameth/index/meta.yml +++ b/modules/bwameth/index/meta.yml @@ -27,6 +27,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/cat/cat/functions.nf b/modules/cat/cat/functions.nf index da9da093..85628ee0 100644 --- a/modules/cat/cat/functions.nf +++ b/modules/cat/cat/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/cat/cat/main.nf b/modules/cat/cat/main.nf index 1c7dbd7c..2dc9944f 100644 --- a/modules/cat/cat/main.nf +++ b/modules/cat/cat/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process CAT_CAT { output: path "${file_out}*" , emit: file_out - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def file_list = files_in.collect { it.toString() } @@ -47,7 +47,10 @@ process CAT_CAT { $command2 \\ > $file_out - echo \$(pigz --version 2>&1) | sed 's/pigz //g' > pigz.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS """ } } diff --git a/modules/cat/cat/meta.yml b/modules/cat/cat/meta.yml index a1318b19..d283107e 100644 --- a/modules/cat/cat/meta.yml +++ b/modules/cat/cat/meta.yml @@ -24,7 +24,7 @@ output: - version: type: file description: File containing version of the pigz software - pattern: "*.{version.txt}" + pattern: "versions.yml" - file_out: type: file description: Concatenated file. Will be gzipped if file_out ends with ".gz" diff --git a/modules/cat/fastq/functions.nf b/modules/cat/fastq/functions.nf index da9da093..85628ee0 100644 --- a/modules/cat/fastq/functions.nf +++ b/modules/cat/fastq/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/chromap/chromap/functions.nf b/modules/chromap/chromap/functions.nf index da9da093..85628ee0 100644 --- a/modules/chromap/chromap/functions.nf +++ b/modules/chromap/chromap/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf index be60c6bd..cbee7fc0 100644 --- a/modules/chromap/chromap/main.nf +++ b/modules/chromap/chromap/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -34,7 +34,7 @@ process CHROMAP_CHROMAP { tuple val(meta), path("*.bam") , optional:true, emit: bam tuple val(meta), path("*.tagAlign.gz"), optional:true, emit: tagAlign tuple val(meta), path("*.pairs.gz") , optional:true, emit: pairs - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -75,7 +75,10 @@ process CHROMAP_CHROMAP { -1 ${reads.join(',')} \\ -o ${prefix}.${file_extension} - echo "$VERSION" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo "$VERSION") + END_VERSIONS """ + compression_cmds } else { """ @@ -87,7 +90,10 @@ process CHROMAP_CHROMAP { -2 ${reads[1]} \\ -o ${prefix}.${file_extension} - echo "$VERSION" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo "$VERSION") + END_VERSIONS """ + compression_cmds } } diff --git a/modules/chromap/chromap/meta.yml b/modules/chromap/chromap/meta.yml index c088ab35..d52e4202 100644 --- a/modules/chromap/chromap/meta.yml +++ b/modules/chromap/chromap/meta.yml @@ -66,7 +66,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bed: type: file description: BED file diff --git a/modules/chromap/index/functions.nf b/modules/chromap/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/chromap/index/functions.nf +++ b/modules/chromap/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/chromap/index/main.nf b/modules/chromap/index/main.nf index c8a75935..764eefe1 100644 --- a/modules/chromap/index/main.nf +++ b/modules/chromap/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process CHROMAP_INDEX { output: path "*.index" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process CHROMAP_INDEX { -t $task.cpus \\ -r $fasta \\ -o ${prefix}.index - echo "$VERSION" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo "$VERSION") + END_VERSIONS """ } diff --git a/modules/chromap/index/meta.yml b/modules/chromap/index/meta.yml index 6a86fbeb..0b3aba75 100644 --- a/modules/chromap/index/meta.yml +++ b/modules/chromap/index/meta.yml @@ -23,7 +23,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - index: type: file description: Index file of the reference genome diff --git a/modules/cnvkit/functions.nf b/modules/cnvkit/functions.nf index da9da093..85628ee0 100755 --- a/modules/cnvkit/functions.nf +++ b/modules/cnvkit/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/cnvkit/main.nf b/modules/cnvkit/main.nf index 4416919e..1219584c 100755 --- a/modules/cnvkit/main.nf +++ b/modules/cnvkit/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -28,7 +28,7 @@ process CNVKIT { tuple val(meta), path("*.cnn"), emit: cnn tuple val(meta), path("*.cnr"), emit: cnr tuple val(meta), path("*.cns"), emit: cns - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,6 +41,9 @@ process CNVKIT { --targets $targetfile \\ $options.args - echo \$(cnvkit.py version) | sed -e "s/cnvkit v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(cnvkit.py version | sed -e "s/cnvkit v//g") + END_VERSIONS """ } diff --git a/modules/cnvkit/meta.yml b/modules/cnvkit/meta.yml index d3d81ecc..5094308f 100755 --- a/modules/cnvkit/meta.yml +++ b/modules/cnvkit/meta.yml @@ -78,7 +78,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@kaurravneet4123" - "@KevinMenden" diff --git a/modules/cooler/digest/functions.nf b/modules/cooler/digest/functions.nf index da9da093..85628ee0 100644 --- a/modules/cooler/digest/functions.nf +++ b/modules/cooler/digest/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/cooler/digest/main.nf b/modules/cooler/digest/main.nf index bb4081d9..ee8b347e 100644 --- a/modules/cooler/digest/main.nf +++ b/modules/cooler/digest/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process COOLER_DIGEST { output: path "*.bed" , emit: bed - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process COOLER_DIGEST { $fasta \\ $enzyme - echo \$(cooler --version 2>&1) | sed 's/cooler, version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(cooler --version 2>&1 | sed 's/cooler, version //') + END_VERSIONS """ } diff --git a/modules/cooler/digest/meta.yml b/modules/cooler/digest/meta.yml index 4623adda..f46fbaff 100644 --- a/modules/cooler/digest/meta.yml +++ b/modules/cooler/digest/meta.yml @@ -29,7 +29,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bed: type: file description: A genome segmentation of restriction fragments as a BED file. diff --git a/modules/cooler/dump/functions.nf b/modules/cooler/dump/functions.nf index da9da093..85628ee0 100644 --- a/modules/cooler/dump/functions.nf +++ b/modules/cooler/dump/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/cooler/dump/main.nf b/modules/cooler/dump/main.nf index c381722c..7d456107 100644 --- a/modules/cooler/dump/main.nf +++ b/modules/cooler/dump/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process COOLER_DUMP { output: tuple val(meta), path("*.bedpe"), emit: bedpe - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process COOLER_DUMP { -o ${prefix}.bedpe \\ $cool - echo \$(cooler --version 2>&1) | sed 's/cooler, version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(cooler --version 2>&1 | sed 's/cooler, version //') + END_VERSIONS """ } diff --git a/modules/cooler/dump/meta.yml b/modules/cooler/dump/meta.yml index 0b2fcc60..ab2d0356 100644 --- a/modules/cooler/dump/meta.yml +++ b/modules/cooler/dump/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bedpe: type: file description: Output text file diff --git a/modules/cutadapt/functions.nf b/modules/cutadapt/functions.nf index da9da093..85628ee0 100644 --- a/modules/cutadapt/functions.nf +++ b/modules/cutadapt/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/cutadapt/main.nf b/modules/cutadapt/main.nf index 6dccc2bc..3baf9c7f 100644 --- a/modules/cutadapt/main.nf +++ b/modules/cutadapt/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process CUTADAPT { output: tuple val(meta), path('*.trim.fastq.gz'), emit: reads tuple val(meta), path('*.log') , emit: log - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process CUTADAPT { $trimmed \\ $reads \\ > ${prefix}.cutadapt.log - echo \$(cutadapt --version) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(cutadapt --version) + END_VERSIONS """ } diff --git a/modules/cutadapt/meta.yml b/modules/cutadapt/meta.yml index 14652343..87276306 100644 --- a/modules/cutadapt/meta.yml +++ b/modules/cutadapt/meta.yml @@ -39,7 +39,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/damageprofiler/functions.nf b/modules/damageprofiler/functions.nf index da9da093..85628ee0 100644 --- a/modules/damageprofiler/functions.nf +++ b/modules/damageprofiler/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/damageprofiler/main.nf b/modules/damageprofiler/main.nf index b370ae3b..cbb27944 100644 --- a/modules/damageprofiler/main.nf +++ b/modules/damageprofiler/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process DAMAGEPROFILER { output: tuple val(meta), path("${prefix}"), emit: results - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process DAMAGEPROFILER { $options.args - echo \$(damageprofiler -v) | sed 's/^DamageProfiler v//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(damageprofiler -v | sed 's/^DamageProfiler v//') + END_VERSIONS """ } diff --git a/modules/damageprofiler/meta.yml b/modules/damageprofiler/meta.yml index b32b9bff..9451f1b2 100644 --- a/modules/damageprofiler/meta.yml +++ b/modules/damageprofiler/meta.yml @@ -43,7 +43,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - results: type: dir description: DamageProfiler results directory diff --git a/modules/deeptools/computematrix/functions.nf b/modules/deeptools/computematrix/functions.nf index da9da093..85628ee0 100644 --- a/modules/deeptools/computematrix/functions.nf +++ b/modules/deeptools/computematrix/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/deeptools/computematrix/main.nf b/modules/deeptools/computematrix/main.nf index 739e7cc1..21a18526 100644 --- a/modules/deeptools/computematrix/main.nf +++ b/modules/deeptools/computematrix/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process DEEPTOOLS_COMPUTEMATRIX { output: tuple val(meta), path("*.mat.gz") , emit: matrix tuple val(meta), path("*.mat.tab"), emit: table - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process DEEPTOOLS_COMPUTEMATRIX { --outFileNameMatrix ${prefix}.computeMatrix.vals.mat.tab \\ --numberOfProcessors $task.cpus - computeMatrix --version | sed -e "s/computeMatrix //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(computeMatrix --version | sed -e "s/computeMatrix //g") + END_VERSIONS """ } diff --git a/modules/deeptools/computematrix/meta.yml b/modules/deeptools/computematrix/meta.yml index d6fd78c7..e3b0282d 100644 --- a/modules/deeptools/computematrix/meta.yml +++ b/modules/deeptools/computematrix/meta.yml @@ -49,7 +49,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@jeremy1805" diff --git a/modules/deeptools/plotfingerprint/functions.nf b/modules/deeptools/plotfingerprint/functions.nf index da9da093..85628ee0 100644 --- a/modules/deeptools/plotfingerprint/functions.nf +++ b/modules/deeptools/plotfingerprint/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/deeptools/plotfingerprint/main.nf b/modules/deeptools/plotfingerprint/main.nf index 56ecb688..9271a399 100644 --- a/modules/deeptools/plotfingerprint/main.nf +++ b/modules/deeptools/plotfingerprint/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process DEEPTOOLS_PLOTFINGERPRINT { tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.raw.txt") , emit: matrix tuple val(meta), path("*.qcmetrics.txt"), emit: metrics - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,6 +41,9 @@ process DEEPTOOLS_PLOTFINGERPRINT { --outQualityMetrics ${prefix}.plotFingerprint.qcmetrics.txt \\ --numberOfProcessors $task.cpus - plotFingerprint --version | sed -e "s/plotFingerprint //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(plotFingerprint --version | sed -e "s/plotFingerprint //g") + END_VERSIONS """ } diff --git a/modules/deeptools/plotfingerprint/meta.yml b/modules/deeptools/plotfingerprint/meta.yml index 6b6f9d8e..6ba88882 100644 --- a/modules/deeptools/plotfingerprint/meta.yml +++ b/modules/deeptools/plotfingerprint/meta.yml @@ -53,7 +53,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@emiller88" diff --git a/modules/deeptools/plotheatmap/functions.nf b/modules/deeptools/plotheatmap/functions.nf index da9da093..85628ee0 100644 --- a/modules/deeptools/plotheatmap/functions.nf +++ b/modules/deeptools/plotheatmap/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/deeptools/plotheatmap/main.nf b/modules/deeptools/plotheatmap/main.nf index 8e25d96f..49362666 100644 --- a/modules/deeptools/plotheatmap/main.nf +++ b/modules/deeptools/plotheatmap/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process DEEPTOOLS_PLOTHEATMAP { output: tuple val(meta), path("*.pdf"), emit: pdf tuple val(meta), path("*.tab"), emit: table - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process DEEPTOOLS_PLOTHEATMAP { --outFileName ${prefix}.plotHeatmap.pdf \\ --outFileNameMatrix ${prefix}.plotHeatmap.mat.tab - plotHeatmap --version | sed -e "s/plotHeatmap //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(plotHeatmap --version | sed -e "s/plotHeatmap //g") + END_VERSIONS """ } diff --git a/modules/deeptools/plotheatmap/meta.yml b/modules/deeptools/plotheatmap/meta.yml index 14311332..97af67f6 100644 --- a/modules/deeptools/plotheatmap/meta.yml +++ b/modules/deeptools/plotheatmap/meta.yml @@ -47,7 +47,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@emiller88" diff --git a/modules/deeptools/plotprofile/functions.nf b/modules/deeptools/plotprofile/functions.nf index da9da093..85628ee0 100644 --- a/modules/deeptools/plotprofile/functions.nf +++ b/modules/deeptools/plotprofile/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/deeptools/plotprofile/main.nf b/modules/deeptools/plotprofile/main.nf index 95f65c84..cba8e161 100644 --- a/modules/deeptools/plotprofile/main.nf +++ b/modules/deeptools/plotprofile/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process DEEPTOOLS_PLOTPROFILE { output: tuple val(meta), path("*.pdf"), emit: pdf tuple val(meta), path("*.tab"), emit: table - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process DEEPTOOLS_PLOTPROFILE { --outFileName ${prefix}.plotProfile.pdf \\ --outFileNameData ${prefix}.plotProfile.tab - plotProfile --version | sed -e "s/plotProfile //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(plotProfile --version | sed -e "s/plotProfile //g") + END_VERSIONS """ } diff --git a/modules/deeptools/plotprofile/meta.yml b/modules/deeptools/plotprofile/meta.yml index 120280de..08fafa49 100644 --- a/modules/deeptools/plotprofile/meta.yml +++ b/modules/deeptools/plotprofile/meta.yml @@ -47,7 +47,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@emiller88" diff --git a/modules/delly/call/functions.nf b/modules/delly/call/functions.nf index da9da093..85628ee0 100644 --- a/modules/delly/call/functions.nf +++ b/modules/delly/call/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/delly/call/main.nf b/modules/delly/call/main.nf index 3bbda48a..f97ddeb0 100644 --- a/modules/delly/call/main.nf +++ b/modules/delly/call/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process DELLY_CALL { output: tuple val(meta), path("*.bcf"), emit: bcf tuple val(meta), path("*.csi"), emit: csi - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process DELLY_CALL { -g $fasta \\ $bam \\ - echo \$(delly --version 2>&1) | sed 's/^.*Delly //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(delly --version 2>&1 | sed 's/^.*Delly //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/delly/call/meta.yml b/modules/delly/call/meta.yml index 9fb79959..16d1a6f2 100644 --- a/modules/delly/call/meta.yml +++ b/modules/delly/call/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bcf: type: file description: BCF format diff --git a/modules/diamond/blastp/functions.nf b/modules/diamond/blastp/functions.nf index da9da093..85628ee0 100644 --- a/modules/diamond/blastp/functions.nf +++ b/modules/diamond/blastp/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf index 88ace780..556f150c 100644 --- a/modules/diamond/blastp/main.nf +++ b/modules/diamond/blastp/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process DIAMOND_BLASTP { output: tuple val(meta), path('*.txt'), emit: txt - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process DIAMOND_BLASTP { $options.args \\ --out ${prefix}.txt - echo \$(diamond --version 2>&1) | tail -n 1 | sed 's/^diamond version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //') + END_VERSIONS """ } diff --git a/modules/diamond/blastp/meta.yml b/modules/diamond/blastp/meta.yml index b6e82f95..e92b1594 100644 --- a/modules/diamond/blastp/meta.yml +++ b/modules/diamond/blastp/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@spficklin" diff --git a/modules/diamond/blastx/functions.nf b/modules/diamond/blastx/functions.nf index da9da093..85628ee0 100644 --- a/modules/diamond/blastx/functions.nf +++ b/modules/diamond/blastx/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf index cd9e4838..8b0227a2 100644 --- a/modules/diamond/blastx/main.nf +++ b/modules/diamond/blastx/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process DIAMOND_BLASTX { output: tuple val(meta), path('*.txt'), emit: txt - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process DIAMOND_BLASTX { $options.args \\ --out ${prefix}.txt - echo \$(diamond --version 2>&1) | tail -n 1 | sed 's/^diamond version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //') + END_VERSIONS """ } diff --git a/modules/diamond/blastx/meta.yml b/modules/diamond/blastx/meta.yml index d9670bed..6e92a336 100644 --- a/modules/diamond/blastx/meta.yml +++ b/modules/diamond/blastx/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@spficklin" diff --git a/modules/diamond/makedb/functions.nf b/modules/diamond/makedb/functions.nf index da9da093..85628ee0 100644 --- a/modules/diamond/makedb/functions.nf +++ b/modules/diamond/makedb/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/diamond/makedb/main.nf b/modules/diamond/makedb/main.nf index 3537d0aa..27383955 100644 --- a/modules/diamond/makedb/main.nf +++ b/modules/diamond/makedb/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process DIAMOND_MAKEDB { output: path "${fasta}.dmnd", emit: db - path '*.version.txt', emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process DIAMOND_MAKEDB { -d $fasta \\ $options.args - echo \$(diamond --version 2>&1) | tail -n 1 | sed 's/^diamond version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //') + END_VERSIONS """ } diff --git a/modules/diamond/makedb/meta.yml b/modules/diamond/makedb/meta.yml index edb63fab..4d8cb695 100644 --- a/modules/diamond/makedb/meta.yml +++ b/modules/diamond/makedb/meta.yml @@ -28,7 +28,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@spficklin" diff --git a/modules/dragonflye/functions.nf b/modules/dragonflye/functions.nf index da9da093..85628ee0 100644 --- a/modules/dragonflye/functions.nf +++ b/modules/dragonflye/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/dragonflye/main.nf b/modules/dragonflye/main.nf index cd0195e9..090c9a13 100644 --- a/modules/dragonflye/main.nf +++ b/modules/dragonflye/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process DRAGONFLYE { tuple val(meta), path("{flye,miniasm,raven}.fasta") , emit: raw_contigs tuple val(meta), path("{miniasm,raven}-unpolished.gfa"), optional:true , emit: gfa tuple val(meta), path("flye-info.txt"), optional:true , emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -40,6 +40,9 @@ process DRAGONFLYE { --ram $memory \\ --outdir ./ \\ --force - echo \$(dragonflye --version 2>&1) | sed 's/^.*dragonflye //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(dragonflye --version 2>&1 | sed 's/^.*dragonflye //' ) + END_VERSIONS """ } diff --git a/modules/dragonflye/meta.yml b/modules/dragonflye/meta.yml index a2bf2703..9affa2f3 100644 --- a/modules/dragonflye/meta.yml +++ b/modules/dragonflye/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - contigs: type: file description: The final assembly produced by Dragonflye diff --git a/modules/dshbio/exportsegments/functions.nf b/modules/dshbio/exportsegments/functions.nf index da9da093..85628ee0 100644 --- a/modules/dshbio/exportsegments/functions.nf +++ b/modules/dshbio/exportsegments/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/dshbio/exportsegments/main.nf b/modules/dshbio/exportsegments/main.nf index bf4c9699..6016f777 100644 --- a/modules/dshbio/exportsegments/main.nf +++ b/modules/dshbio/exportsegments/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process DSHBIO_EXPORTSEGMENTS { output: tuple val(meta), path("*.fa"), emit: fasta - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process DSHBIO_EXPORTSEGMENTS { -i $gfa \\ -o ${prefix}.fa - echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(dsh-bio --version 2>&1 | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ') + END_VERSIONS """ } diff --git a/modules/dshbio/exportsegments/meta.yml b/modules/dshbio/exportsegments/meta.yml index c064527e..c57a6179 100644 --- a/modules/dshbio/exportsegments/meta.yml +++ b/modules/dshbio/exportsegments/meta.yml @@ -35,6 +35,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@heuermh" diff --git a/modules/dshbio/filterbed/functions.nf b/modules/dshbio/filterbed/functions.nf index da9da093..85628ee0 100644 --- a/modules/dshbio/filterbed/functions.nf +++ b/modules/dshbio/filterbed/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/dshbio/filterbed/main.nf b/modules/dshbio/filterbed/main.nf index cc1daa7d..3f2a068d 100644 --- a/modules/dshbio/filterbed/main.nf +++ b/modules/dshbio/filterbed/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process DSHBIO_FILTERBED { output: tuple val(meta), path("*.bed.gz"), emit: bed - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process DSHBIO_FILTERBED { -i $bed \\ -o ${prefix}.bed.gz - echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(dsh-bio --version 2>&1 | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ') + END_VERSIONS """ } diff --git a/modules/dshbio/filterbed/meta.yml b/modules/dshbio/filterbed/meta.yml index 61626ead..5545aac1 100644 --- a/modules/dshbio/filterbed/meta.yml +++ b/modules/dshbio/filterbed/meta.yml @@ -33,6 +33,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@heuermh" diff --git a/modules/dshbio/filtergff3/functions.nf b/modules/dshbio/filtergff3/functions.nf index da9da093..85628ee0 100644 --- a/modules/dshbio/filtergff3/functions.nf +++ b/modules/dshbio/filtergff3/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/dshbio/filtergff3/main.nf b/modules/dshbio/filtergff3/main.nf index 596c6b8f..2a1ad816 100644 --- a/modules/dshbio/filtergff3/main.nf +++ b/modules/dshbio/filtergff3/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process DSHBIO_FILTERGFF3 { output: tuple val(meta), path("*.gff3.gz"), emit: gff3 - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process DSHBIO_FILTERGFF3 { -i $gff3 \\ -o ${prefix}.gff3.gz - echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(dsh-bio --version 2>&1 | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ') + END_VERSIONS """ } diff --git a/modules/dshbio/filtergff3/meta.yml b/modules/dshbio/filtergff3/meta.yml index 3f89d71b..d1b7a509 100644 --- a/modules/dshbio/filtergff3/meta.yml +++ b/modules/dshbio/filtergff3/meta.yml @@ -33,6 +33,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@heuermh" diff --git a/modules/dshbio/splitbed/functions.nf b/modules/dshbio/splitbed/functions.nf index da9da093..85628ee0 100644 --- a/modules/dshbio/splitbed/functions.nf +++ b/modules/dshbio/splitbed/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/dshbio/splitbed/main.nf b/modules/dshbio/splitbed/main.nf index 75307b14..388ba0ef 100644 --- a/modules/dshbio/splitbed/main.nf +++ b/modules/dshbio/splitbed/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process DSHBIO_SPLITBED { output: tuple val(meta), path("*.bed.gz"), emit: bed - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process DSHBIO_SPLITBED { -s '.bed.gz' \\ -i $bed - echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(dsh-bio --version 2>&1 | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ') + END_VERSIONS """ } diff --git a/modules/dshbio/splitbed/meta.yml b/modules/dshbio/splitbed/meta.yml index f2257812..0c4788a1 100644 --- a/modules/dshbio/splitbed/meta.yml +++ b/modules/dshbio/splitbed/meta.yml @@ -33,6 +33,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@heuermh" diff --git a/modules/dshbio/splitgff3/functions.nf b/modules/dshbio/splitgff3/functions.nf index da9da093..85628ee0 100644 --- a/modules/dshbio/splitgff3/functions.nf +++ b/modules/dshbio/splitgff3/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/dshbio/splitgff3/main.nf b/modules/dshbio/splitgff3/main.nf index fa434b75..b8f81392 100644 --- a/modules/dshbio/splitgff3/main.nf +++ b/modules/dshbio/splitgff3/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process DSHBIO_SPLITGFF3 { output: tuple val(meta), path("*.gff3.gz"), emit: gff3 - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process DSHBIO_SPLITGFF3 { -s '.gff3.gz' \\ -i $gff3 - echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(dsh-bio --version 2>&1 | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ') + END_VERSIONS """ } diff --git a/modules/dshbio/splitgff3/meta.yml b/modules/dshbio/splitgff3/meta.yml index 46118bb7..1bdfa652 100644 --- a/modules/dshbio/splitgff3/meta.yml +++ b/modules/dshbio/splitgff3/meta.yml @@ -33,6 +33,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@heuermh" diff --git a/modules/ensemblvep/functions.nf b/modules/ensemblvep/functions.nf index da9da093..85628ee0 100644 --- a/modules/ensemblvep/functions.nf +++ b/modules/ensemblvep/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/ensemblvep/main.nf b/modules/ensemblvep/main.nf index c2194e77..32acc4dd 100644 --- a/modules/ensemblvep/main.nf +++ b/modules/ensemblvep/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -33,7 +33,7 @@ process ENSEMBLVEP { output: tuple val(meta), path("*.ann.vcf"), emit: vcf path "*.summary.html" , emit: report - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -57,6 +57,9 @@ process ENSEMBLVEP { rm -rf $prefix - echo \$(vep --help 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(vep --help 2>&1) + END_VERSIONS """ } diff --git a/modules/ensemblvep/meta.yml b/modules/ensemblvep/meta.yml index 5eb111e9..e97c5609 100644 --- a/modules/ensemblvep/meta.yml +++ b/modules/ensemblvep/meta.yml @@ -59,6 +59,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@maxulysse" diff --git a/modules/expansionhunter/functions.nf b/modules/expansionhunter/functions.nf index da9da093..85628ee0 100644 --- a/modules/expansionhunter/functions.nf +++ b/modules/expansionhunter/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/expansionhunter/main.nf b/modules/expansionhunter/main.nf index 41c6ed6c..7ee97c5a 100644 --- a/modules/expansionhunter/main.nf +++ b/modules/expansionhunter/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process EXPANSIONHUNTER { output: tuple val(meta), path("*.vcf"), emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -40,6 +40,9 @@ process EXPANSIONHUNTER { --variant-catalog $variant_catalog \\ --sex $gender - echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(ExpansionHunter --version 2>&1 | sed 's/^.*ExpansionHunter //') + END_VERSIONS """ } diff --git a/modules/expansionhunter/meta.yml b/modules/expansionhunter/meta.yml index cac3ed2b..a5733d93 100644 --- a/modules/expansionhunter/meta.yml +++ b/modules/expansionhunter/meta.yml @@ -40,7 +40,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - vcf: type: file description: VCF with repeat expansions diff --git a/modules/fastani/functions.nf b/modules/fastani/functions.nf index da9da093..85628ee0 100644 --- a/modules/fastani/functions.nf +++ b/modules/fastani/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/fastani/main.nf b/modules/fastani/main.nf index 11916a65..7ee35a0d 100644 --- a/modules/fastani/main.nf +++ b/modules/fastani/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process FASTANI { output: tuple val(meta), path("*.ani.txt"), emit: ani - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,7 +37,10 @@ process FASTANI { -rl $reference \\ -o ${prefix}.ani.txt - echo \$(fastANI --version 2>&1) | sed 's/version//;' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(fastANI --version 2>&1 | sed 's/version//;') + END_VERSIONS """ } else { """ @@ -46,7 +49,10 @@ process FASTANI { -r $reference \\ -o ${prefix}.ani.txt - echo \$(fastANI --version 2>&1) | sed 's/version//;' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(fastANI --version 2>&1 | sed 's/version//;') + END_VERSIONS """ } } diff --git a/modules/fastani/meta.yml b/modules/fastani/meta.yml index ed6be165..783ae068 100644 --- a/modules/fastani/meta.yml +++ b/modules/fastani/meta.yml @@ -38,6 +38,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@abhi18av" diff --git a/modules/fastp/functions.nf b/modules/fastp/functions.nf index da9da093..85628ee0 100644 --- a/modules/fastp/functions.nf +++ b/modules/fastp/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/fastp/main.nf b/modules/fastp/main.nf index 652ffe80..11cd30b4 100644 --- a/modules/fastp/main.nf +++ b/modules/fastp/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -28,7 +28,7 @@ process FASTP { tuple val(meta), path('*.json') , emit: json tuple val(meta), path('*.html') , emit: html tuple val(meta), path('*.log') , emit: log - path '*.version.txt' , emit: version + path "versions.yml" , emit: version tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged @@ -49,7 +49,10 @@ process FASTP { $fail_fastq \\ $options.args \\ 2> ${prefix}.fastp.log - echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(fastp --version 2>&1 | sed -e "s/fastp //g") + END_VERSIONS """ } else { def fail_fastq = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : '' @@ -71,7 +74,10 @@ process FASTP { $options.args \\ 2> ${prefix}.fastp.log - echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(fastp --version 2>&1 | sed -e "s/fastp //g") + END_VERSIONS """ } } diff --git a/modules/fastp/meta.yml b/modules/fastp/meta.yml index d9130d6d..72ddb7d7 100644 --- a/modules/fastp/meta.yml +++ b/modules/fastp/meta.yml @@ -47,7 +47,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - reads_fail: type: file description: Reads the failed the preprocessing diff --git a/modules/fasttree/functions.nf b/modules/fasttree/functions.nf index da9da093..85628ee0 100644 --- a/modules/fasttree/functions.nf +++ b/modules/fasttree/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/fasttree/main.nf b/modules/fasttree/main.nf index f0bacb87..08c093b2 100644 --- a/modules/fasttree/main.nf +++ b/modules/fasttree/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -22,7 +22,7 @@ process FASTTREE { output: path "*.tre", emit: phylogeny - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process FASTTREE { -nt $alignment \\ > fasttree_phylogeny.tre - echo \$(fasttree -help 2>&1) | head -1 | sed 's/^FastTree \\([0-9\\.]*\\) .*\$/\\1/' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(fasttree -help 2>&1 | head -1 | sed 's/^FastTree \\([0-9\\.]*\\) .*\$/\\1/') + END_VERSIONS """ } diff --git a/modules/fasttree/meta.yml b/modules/fasttree/meta.yml index 5912395d..70000030 100644 --- a/modules/fasttree/meta.yml +++ b/modules/fasttree/meta.yml @@ -22,7 +22,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - phylogeny: type: file description: A phylogeny in Newick format diff --git a/modules/fgbio/callmolecularconsensusreads/functions.nf b/modules/fgbio/callmolecularconsensusreads/functions.nf index da9da093..85628ee0 100644 --- a/modules/fgbio/callmolecularconsensusreads/functions.nf +++ b/modules/fgbio/callmolecularconsensusreads/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/fgbio/callmolecularconsensusreads/main.nf index a530ba55..ba099d8d 100644 --- a/modules/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/fgbio/callmolecularconsensusreads/main.nf @@ -1,4 +1,4 @@ -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -22,7 +22,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { -i $bam \\ $options.args \\ -o ${prefix}.bam - fgbio --version | sed -e "s/fgbio v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(fgbio --version | sed -e "s/fgbio v//g") + END_VERSIONS """ } diff --git a/modules/fgbio/callmolecularconsensusreads/meta.yml b/modules/fgbio/callmolecularconsensusreads/meta.yml index 5f80bce9..3e62c3a6 100644 --- a/modules/fgbio/callmolecularconsensusreads/meta.yml +++ b/modules/fgbio/callmolecularconsensusreads/meta.yml @@ -39,7 +39,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@sruthipsuresh" diff --git a/modules/fgbio/sortbam/functions.nf b/modules/fgbio/sortbam/functions.nf index da9da093..85628ee0 100644 --- a/modules/fgbio/sortbam/functions.nf +++ b/modules/fgbio/sortbam/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/fgbio/sortbam/main.nf b/modules/fgbio/sortbam/main.nf index 798d5f23..81ac89c2 100644 --- a/modules/fgbio/sortbam/main.nf +++ b/modules/fgbio/sortbam/main.nf @@ -1,4 +1,4 @@ -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -22,7 +22,7 @@ process FGBIO_SORTBAM { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,7 +33,10 @@ process FGBIO_SORTBAM { -i $bam \\ $options.args \\ -o ${prefix}.bam - fgbio --version | sed -e "s/fgbio v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(fgbio --version | sed -e "s/fgbio v//g") + END_VERSIONS """ } diff --git a/modules/fgbio/sortbam/meta.yml b/modules/fgbio/sortbam/meta.yml index 9e68dac4..def106c3 100644 --- a/modules/fgbio/sortbam/meta.yml +++ b/modules/fgbio/sortbam/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@sruthipsuresh" diff --git a/modules/flash/functions.nf b/modules/flash/functions.nf index da9da093..85628ee0 100644 --- a/modules/flash/functions.nf +++ b/modules/flash/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/flash/main.nf b/modules/flash/main.nf index acdc10a7..8b8d99e4 100644 --- a/modules/flash/main.nf +++ b/modules/flash/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -22,7 +22,7 @@ process FLASH { output: tuple val(meta), path("*.merged.*.fastq.gz"), emit: reads - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process FLASH { $merged \\ -z \\ $input_reads - echo \$(flash --version) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(flash --version) + END_VERSIONS """ } diff --git a/modules/flash/meta.yml b/modules/flash/meta.yml index ff747912..62d40e20 100644 --- a/modules/flash/meta.yml +++ b/modules/flash/meta.yml @@ -38,7 +38,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@Erkison" diff --git a/modules/gatk4/applybqsr/functions.nf b/modules/gatk4/applybqsr/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/applybqsr/functions.nf +++ b/modules/gatk4/applybqsr/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf index 19b8c3d6..9c51ce60 100644 --- a/modules/gatk4/applybqsr/main.nf +++ b/modules/gatk4/applybqsr/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process GATK4_APPLYBQSR { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process GATK4_APPLYBQSR { -O ${prefix}.bam \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/applybqsr/meta.yml b/modules/gatk4/applybqsr/meta.yml index 9bf12f09..b0177c76 100644 --- a/modules/gatk4/applybqsr/meta.yml +++ b/modules/gatk4/applybqsr/meta.yml @@ -48,7 +48,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: Recalibrated BAM file diff --git a/modules/gatk4/baserecalibrator/functions.nf b/modules/gatk4/baserecalibrator/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/baserecalibrator/functions.nf +++ b/modules/gatk4/baserecalibrator/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf index 4e2730f2..9abca6e9 100644 --- a/modules/gatk4/baserecalibrator/main.nf +++ b/modules/gatk4/baserecalibrator/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -29,7 +29,7 @@ process GATK4_BASERECALIBRATOR { output: tuple val(meta), path("*.table"), emit: table - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -45,6 +45,9 @@ process GATK4_BASERECALIBRATOR { $options.args \ -O ${prefix}.table - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/baserecalibrator/meta.yml b/modules/gatk4/baserecalibrator/meta.yml index 0996dcbe..a5bac064 100644 --- a/modules/gatk4/baserecalibrator/meta.yml +++ b/modules/gatk4/baserecalibrator/meta.yml @@ -48,7 +48,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - table: type: file description: Recalibration table from BaseRecalibrator diff --git a/modules/gatk4/bedtointervallist/functions.nf b/modules/gatk4/bedtointervallist/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/bedtointervallist/functions.nf +++ b/modules/gatk4/bedtointervallist/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf index af385f8f..fc484f84 100644 --- a/modules/gatk4/bedtointervallist/main.nf +++ b/modules/gatk4/bedtointervallist/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process GATK4_BEDTOINTERVALLIST { output: tuple val(meta), path('*.interval_list'), emit: interval_list - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process GATK4_BEDTOINTERVALLIST { -O ${prefix}.interval_list \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/bedtointervallist/meta.yml b/modules/gatk4/bedtointervallist/meta.yml index 23e98447..28fd5d22 100644 --- a/modules/gatk4/bedtointervallist/meta.yml +++ b/modules/gatk4/bedtointervallist/meta.yml @@ -34,6 +34,6 @@ output: - version: type: file description: File containing software version - pattern: "*.version.txt" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/gatk4/createsequencedictionary/functions.nf b/modules/gatk4/createsequencedictionary/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/createsequencedictionary/functions.nf +++ b/modules/gatk4/createsequencedictionary/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf index 0276e8b2..0c0446c6 100644 --- a/modules/gatk4/createsequencedictionary/main.nf +++ b/modules/gatk4/createsequencedictionary/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process GATK4_CREATESEQUENCEDICTIONARY { output: path "*.dict" , emit: dict - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -40,6 +40,9 @@ process GATK4_CREATESEQUENCEDICTIONARY { --URI $fasta \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/createsequencedictionary/meta.yml b/modules/gatk4/createsequencedictionary/meta.yml index d0cc5980..21bdc599 100644 --- a/modules/gatk4/createsequencedictionary/meta.yml +++ b/modules/gatk4/createsequencedictionary/meta.yml @@ -25,6 +25,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@maxulysse" diff --git a/modules/gatk4/fastqtosam/functions.nf b/modules/gatk4/fastqtosam/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/fastqtosam/functions.nf +++ b/modules/gatk4/fastqtosam/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf index e00f34f5..e7b38f35 100644 --- a/modules/gatk4/fastqtosam/main.nf +++ b/modules/gatk4/fastqtosam/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process GATK4_FASTQTOSAM { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process GATK4_FASTQTOSAM { -SM $prefix \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/fastqtosam/meta.yml b/modules/gatk4/fastqtosam/meta.yml index d574d67b..4ae9eeaa 100644 --- a/modules/gatk4/fastqtosam/meta.yml +++ b/modules/gatk4/fastqtosam/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: Converted BAM file diff --git a/modules/gatk4/getpileupsummaries/functions.nf b/modules/gatk4/getpileupsummaries/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/getpileupsummaries/functions.nf +++ b/modules/gatk4/getpileupsummaries/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf index 9ae95d9c..da03555c 100644 --- a/modules/gatk4/getpileupsummaries/main.nf +++ b/modules/gatk4/getpileupsummaries/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process GATK4_GETPILEUPSUMMARIES { output: tuple val(meta), path('*.pileups.table'), emit: table - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -43,6 +43,9 @@ process GATK4_GETPILEUPSUMMARIES { -O ${prefix}.pileups.table \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/getpileupsummaries/meta.yml b/modules/gatk4/getpileupsummaries/meta.yml index e784595a..5bb87e80 100644 --- a/modules/gatk4/getpileupsummaries/meta.yml +++ b/modules/gatk4/getpileupsummaries/meta.yml @@ -51,7 +51,7 @@ output: - version: type: file description: File containing software version - pattern: "*.version.txt" + pattern: "versions.yml" authors: - "@GCJMackenzie" diff --git a/modules/gatk4/haplotypecaller/functions.nf b/modules/gatk4/haplotypecaller/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/haplotypecaller/functions.nf +++ b/modules/gatk4/haplotypecaller/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf index c451de7f..02fd1ee3 100644 --- a/modules/gatk4/haplotypecaller/main.nf +++ b/modules/gatk4/haplotypecaller/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process GATK4_HAPLOTYPECALLER { output: tuple val(meta), path("*.vcf.gz"), emit: vcf tuple val(meta), path("*.tbi") , emit: tbi - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -47,6 +47,9 @@ process GATK4_HAPLOTYPECALLER { -O ${prefix}.vcf.gz \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/haplotypecaller/meta.yml b/modules/gatk4/haplotypecaller/meta.yml index f0fc3910..4b8e8387 100644 --- a/modules/gatk4/haplotypecaller/meta.yml +++ b/modules/gatk4/haplotypecaller/meta.yml @@ -49,7 +49,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - vcf: type: file description: Compressed VCF file diff --git a/modules/gatk4/intervallisttools/functions.nf b/modules/gatk4/intervallisttools/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/intervallisttools/functions.nf +++ b/modules/gatk4/intervallisttools/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf index b2486eac..90a77c5a 100644 --- a/modules/gatk4/intervallisttools/main.nf +++ b/modules/gatk4/intervallisttools/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process GATK4_INTERVALLISTTOOLS { output: tuple val(meta), path("*_split/*/*.interval_list"), emit: interval_list - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -48,6 +48,9 @@ process GATK4_INTERVALLISTTOOLS { os.rename(interval, newName) CODE - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/intervallisttools/meta.yml b/modules/gatk4/intervallisttools/meta.yml index efe31da1..65adb7b6 100644 --- a/modules/gatk4/intervallisttools/meta.yml +++ b/modules/gatk4/intervallisttools/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - interval_list: type: file description: Interval list files diff --git a/modules/gatk4/markduplicates/functions.nf b/modules/gatk4/markduplicates/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/markduplicates/functions.nf +++ b/modules/gatk4/markduplicates/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf index 6df2a47c..68b17366 100644 --- a/modules/gatk4/markduplicates/main.nf +++ b/modules/gatk4/markduplicates/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process GATK4_MARKDUPLICATES { output: tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.metrics"), emit: metrics - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process GATK4_MARKDUPLICATES { --OUTPUT ${prefix}.bam \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/markduplicates/meta.yml b/modules/gatk4/markduplicates/meta.yml index abe61e02..58e30910 100644 --- a/modules/gatk4/markduplicates/meta.yml +++ b/modules/gatk4/markduplicates/meta.yml @@ -35,7 +35,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: Marked duplicates BAM file diff --git a/modules/gatk4/mergebamalignment/functions.nf b/modules/gatk4/mergebamalignment/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/mergebamalignment/functions.nf +++ b/modules/gatk4/mergebamalignment/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf index b65f4653..269836a7 100644 --- a/modules/gatk4/mergebamalignment/main.nf +++ b/modules/gatk4/mergebamalignment/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process GATK4_MERGEBAMALIGNMENT { output: tuple val(meta), path('*.bam'), emit: bam - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process GATK4_MERGEBAMALIGNMENT { O=${prefix}.bam \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/mergebamalignment/meta.yml b/modules/gatk4/mergebamalignment/meta.yml index 155b6364..e2e7b7ec 100644 --- a/modules/gatk4/mergebamalignment/meta.yml +++ b/modules/gatk4/mergebamalignment/meta.yml @@ -40,6 +40,6 @@ output: - version: type: file description: File containing software version - pattern: "*.version.txt" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/gatk4/mergevcfs/functions.nf b/modules/gatk4/mergevcfs/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/mergevcfs/functions.nf +++ b/modules/gatk4/mergevcfs/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf index 5a80c9ff..d47aa68f 100644 --- a/modules/gatk4/mergevcfs/main.nf +++ b/modules/gatk4/mergevcfs/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process GATK4_MERGEVCFS { output: tuple val(meta), path('*.vcf.gz'), emit: vcf - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -44,6 +44,9 @@ process GATK4_MERGEVCFS { $ref \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/mergevcfs/meta.yml b/modules/gatk4/mergevcfs/meta.yml index 14b28fa0..d2679ab8 100644 --- a/modules/gatk4/mergevcfs/meta.yml +++ b/modules/gatk4/mergevcfs/meta.yml @@ -37,6 +37,6 @@ output: - version: type: file description: File containing software version - pattern: "*.version.txt" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/gatk4/mutect2/functions.nf b/modules/gatk4/mutect2/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/mutect2/functions.nf +++ b/modules/gatk4/mutect2/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf index 6ab9e1c7..03bcc2d1 100644 --- a/modules/gatk4/mutect2/main.nf +++ b/modules/gatk4/mutect2/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -35,7 +35,7 @@ process GATK4_MUTECT2 { tuple val(meta), path("*.tbi") , emit: tbi tuple val(meta), path("*.stats") , emit: stats tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2 - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -72,6 +72,9 @@ process GATK4_MUTECT2 { -O ${prefix}.vcf.gz \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/mutect2/meta.yml b/modules/gatk4/mutect2/meta.yml index 7833d694..75b38153 100644 --- a/modules/gatk4/mutect2/meta.yml +++ b/modules/gatk4/mutect2/meta.yml @@ -87,7 +87,7 @@ output: - version: type: file description: File containing software version - pattern: "*.version.txt" + pattern: "versions.yml" authors: - "@GCJMackenzie" diff --git a/modules/gatk4/revertsam/functions.nf b/modules/gatk4/revertsam/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/revertsam/functions.nf +++ b/modules/gatk4/revertsam/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf index 2f4959db..e691d3f9 100644 --- a/modules/gatk4/revertsam/main.nf +++ b/modules/gatk4/revertsam/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process GATK4_REVERTSAM { output: tuple val(meta), path('*.bam'), emit: bam - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process GATK4_REVERTSAM { O=${prefix}.reverted.bam \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/revertsam/meta.yml b/modules/gatk4/revertsam/meta.yml index 258bb253..d6a1d7fa 100644 --- a/modules/gatk4/revertsam/meta.yml +++ b/modules/gatk4/revertsam/meta.yml @@ -30,6 +30,6 @@ output: - version: type: file description: File containing software version - pattern: "*.version.txt" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/gatk4/samtofastq/functions.nf b/modules/gatk4/samtofastq/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/samtofastq/functions.nf +++ b/modules/gatk4/samtofastq/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf index 486d6b5d..edf895bb 100644 --- a/modules/gatk4/samtofastq/main.nf +++ b/modules/gatk4/samtofastq/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process GATK4_SAMTOFASTQ { output: tuple val(meta), path('*.fastq.gz'), emit: fastq - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process GATK4_SAMTOFASTQ { $output \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/samtofastq/meta.yml b/modules/gatk4/samtofastq/meta.yml index 0601f3a7..956d2186 100644 --- a/modules/gatk4/samtofastq/meta.yml +++ b/modules/gatk4/samtofastq/meta.yml @@ -30,6 +30,6 @@ output: - version: type: file description: File containing software version - pattern: "*.version.txt" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/gatk4/splitncigarreads/functions.nf b/modules/gatk4/splitncigarreads/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/splitncigarreads/functions.nf +++ b/modules/gatk4/splitncigarreads/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf index a8724e2e..11d6c9a5 100644 --- a/modules/gatk4/splitncigarreads/main.nf +++ b/modules/gatk4/splitncigarreads/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process GATK4_SPLITNCIGARREADS { output: tuple val(meta), path('*.bam'), emit: bam - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process GATK4_SPLITNCIGARREADS { -O ${prefix}.bam \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/splitncigarreads/meta.yml b/modules/gatk4/splitncigarreads/meta.yml index e433cbf6..c4266874 100644 --- a/modules/gatk4/splitncigarreads/meta.yml +++ b/modules/gatk4/splitncigarreads/meta.yml @@ -35,6 +35,6 @@ output: - version: type: file description: File containing software version - pattern: "*.version.txt" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/gatk4/variantfiltration/functions.nf b/modules/gatk4/variantfiltration/functions.nf index da9da093..85628ee0 100644 --- a/modules/gatk4/variantfiltration/functions.nf +++ b/modules/gatk4/variantfiltration/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf index 82593d18..90b6ef25 100644 --- a/modules/gatk4/variantfiltration/main.nf +++ b/modules/gatk4/variantfiltration/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process GATK4_VARIANTFILTRATION { output: tuple val(meta), path("*.vcf"), emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: @@ -39,6 +39,9 @@ process GATK4_VARIANTFILTRATION { -O ${prefix}.vcf \\ $options.args - echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/gatk4/variantfiltration/meta.yml b/modules/gatk4/variantfiltration/meta.yml index d7f72582..6b0a9026 100644 --- a/modules/gatk4/variantfiltration/meta.yml +++ b/modules/gatk4/variantfiltration/meta.yml @@ -42,6 +42,6 @@ output: - version: type: file description: File containing software version - pattern: "*.version.txt" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/genmap/index/functions.nf b/modules/genmap/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/genmap/index/functions.nf +++ b/modules/genmap/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/genmap/index/main.nf b/modules/genmap/index/main.nf index 8166315e..f1168d4e 100644 --- a/modules/genmap/index/main.nf +++ b/modules/genmap/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process GENMAP_INDEX { output: path "genmap" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process GENMAP_INDEX { -F $fasta \\ -I genmap - echo \$(genmap --version 2>&1) | sed 's/GenMap version: //; s/SeqAn.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//') + END_VERSIONS """ } diff --git a/modules/genmap/index/meta.yml b/modules/genmap/index/meta.yml index 332c3ba7..cd299da2 100644 --- a/modules/genmap/index/meta.yml +++ b/modules/genmap/index/meta.yml @@ -21,7 +21,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - index: type: index description: Genmap index file diff --git a/modules/genmap/mappability/functions.nf b/modules/genmap/mappability/functions.nf index da9da093..85628ee0 100644 --- a/modules/genmap/mappability/functions.nf +++ b/modules/genmap/mappability/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/genmap/mappability/main.nf b/modules/genmap/mappability/main.nf index 8587c950..9eeb4253 100644 --- a/modules/genmap/mappability/main.nf +++ b/modules/genmap/mappability/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process GENMAP_MAPPABILITY { path "*.wig" , optional:true, emit: wig path "*.bedgraph" , optional:true, emit: bedgraph path "*.txt" , optional:true, emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process GENMAP_MAPPABILITY { -I $index \\ -O mappability - echo \$(genmap --version 2>&1) | sed 's/GenMap version: //; s/SeqAn.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//') + END_VERSIONS """ } diff --git a/modules/genmap/mappability/meta.yml b/modules/genmap/mappability/meta.yml index 851119c9..90807077 100644 --- a/modules/genmap/mappability/meta.yml +++ b/modules/genmap/mappability/meta.yml @@ -24,7 +24,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - wig: type: file description: genmap wig mappability file diff --git a/modules/gffread/functions.nf b/modules/gffread/functions.nf index da9da093..85628ee0 100644 --- a/modules/gffread/functions.nf +++ b/modules/gffread/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gffread/main.nf b/modules/gffread/main.nf index 6b0dd666..1622e98d 100644 --- a/modules/gffread/main.nf +++ b/modules/gffread/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process GFFREAD { output: path "*.gtf" , emit: gtf - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process GFFREAD { $gff \\ $options.args \\ -o ${prefix}.gtf - echo \$(gffread --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gffread --version 2>&1) + END_VERSIONS """ } diff --git a/modules/gffread/meta.yml b/modules/gffread/meta.yml index af2abb6e..1cb7fc91 100644 --- a/modules/gffread/meta.yml +++ b/modules/gffread/meta.yml @@ -27,7 +27,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@emiller88" diff --git a/modules/glnexus/functions.nf b/modules/glnexus/functions.nf index da9da093..85628ee0 100644 --- a/modules/glnexus/functions.nf +++ b/modules/glnexus/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/glnexus/main.nf b/modules/glnexus/main.nf index dadb9d60..60f50932 100644 --- a/modules/glnexus/main.nf +++ b/modules/glnexus/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process GLNEXUS { output: tuple val(meta), path("*.bcf"), emit: bcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -44,6 +44,9 @@ process GLNEXUS { $options.args \\ ${input.join(' ')} \\ > ${prefix}.bcf - echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(glnexus_cli 2>&1 | head -n 1 | sed 's/^.*release //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/glnexus/meta.yml b/modules/glnexus/meta.yml index f64a812e..fd1a407d 100644 --- a/modules/glnexus/meta.yml +++ b/modules/glnexus/meta.yml @@ -27,7 +27,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bcf: type: file description: merged BCF file diff --git a/modules/graphmap2/align/functions.nf b/modules/graphmap2/align/functions.nf index da9da093..85628ee0 100644 --- a/modules/graphmap2/align/functions.nf +++ b/modules/graphmap2/align/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/graphmap2/align/main.nf b/modules/graphmap2/align/main.nf index 0ee4c02b..cf598b3d 100644 --- a/modules/graphmap2/align/main.nf +++ b/modules/graphmap2/align/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process GRAPHMAP2_ALIGN { output: tuple val(meta), path("*.sam"), emit: sam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,6 +41,9 @@ process GRAPHMAP2_ALIGN { -o ${prefix}.sam \\ $options.args - echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(graphmap2 align 2>&1 | sed 's/^.*Version: v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/graphmap2/align/meta.yml b/modules/graphmap2/align/meta.yml index da773ed2..a5b3cd6c 100644 --- a/modules/graphmap2/align/meta.yml +++ b/modules/graphmap2/align/meta.yml @@ -44,7 +44,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/graphmap2/index/functions.nf b/modules/graphmap2/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/graphmap2/index/functions.nf +++ b/modules/graphmap2/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/graphmap2/index/main.nf b/modules/graphmap2/index/main.nf index 17811d4c..906aa6ec 100644 --- a/modules/graphmap2/index/main.nf +++ b/modules/graphmap2/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -22,7 +22,7 @@ process GRAPHMAP2_INDEX { output: path "*.gmidx" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process GRAPHMAP2_INDEX { $options.args \\ -r $fasta - echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(graphmap2 align 2>&1 | sed 's/^.*Version: v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/graphmap2/index/meta.yml b/modules/graphmap2/index/meta.yml index b74f985a..4ff63276 100644 --- a/modules/graphmap2/index/meta.yml +++ b/modules/graphmap2/index/meta.yml @@ -23,7 +23,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/gubbins/functions.nf b/modules/gubbins/functions.nf index da9da093..85628ee0 100644 --- a/modules/gubbins/functions.nf +++ b/modules/gubbins/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gubbins/main.nf b/modules/gubbins/main.nf index 7f0041c8..10117ae7 100644 --- a/modules/gubbins/main.nf +++ b/modules/gubbins/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -30,7 +30,7 @@ process GUBBINS { path "*.branch_base_reconstruction.embl", emit: embl_branch path "*.final_tree.tre" , emit: tree path "*.node_labelled.final_tree.tre" , emit: tree_labelled - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process GUBBINS { --threads $task.cpus \\ $options.args \\ $alignment - echo \$(run_gubbins.py --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(run_gubbins.py --version 2>&1) + END_VERSIONS """ } diff --git a/modules/gubbins/meta.yml b/modules/gubbins/meta.yml index d1410afb..1a49b335 100644 --- a/modules/gubbins/meta.yml +++ b/modules/gubbins/meta.yml @@ -19,7 +19,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - fasta: type: file description: Filtered variant alignment in fasta format diff --git a/modules/gunzip/functions.nf b/modules/gunzip/functions.nf index da9da093..85628ee0 100644 --- a/modules/gunzip/functions.nf +++ b/modules/gunzip/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/gunzip/main.nf b/modules/gunzip/main.nf index 29248796..a53a9858 100644 --- a/modules/gunzip/main.nf +++ b/modules/gunzip/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process GUNZIP { output: path "$gunzip", emit: gunzip - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) gunzip = archive.toString() - '.gz' """ gunzip -f $options.args $archive - echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(gunzip --version 2>&1 | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS """ } diff --git a/modules/gunzip/meta.yml b/modules/gunzip/meta.yml index 922e74e6..60911685 100644 --- a/modules/gunzip/meta.yml +++ b/modules/gunzip/meta.yml @@ -21,7 +21,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/hifiasm/functions.nf b/modules/hifiasm/functions.nf index da9da093..85628ee0 100644 --- a/modules/hifiasm/functions.nf +++ b/modules/hifiasm/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/hifiasm/main.nf b/modules/hifiasm/main.nf index 5d005ee4..2597afa9 100644 --- a/modules/hifiasm/main.nf +++ b/modules/hifiasm/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -34,7 +34,7 @@ process HIFIASM { tuple val(meta), path("*.asm.a_ctg.gfa") , emit: alternate_contigs, optional: true tuple val(meta), path("*.hap1.p_ctg.gfa") , emit: paternal_contigs , optional: true tuple val(meta), path("*.hap2.p_ctg.gfa") , emit: maternal_contigs , optional: true - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -49,7 +49,10 @@ process HIFIASM { -2 $maternal_kmer_dump \\ $reads - echo \$(hifiasm --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(hifiasm --version 2>&1) + END_VERSIONS """ } else { // Phasing with Hi-C data is not supported yet """ @@ -59,7 +62,10 @@ process HIFIASM { -t $task.cpus \\ $reads - echo \$(hifiasm --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(hifiasm --version 2>&1) + END_VERSIONS """ } } diff --git a/modules/hifiasm/meta.yml b/modules/hifiasm/meta.yml index dc414b93..c6d5a735 100644 --- a/modules/hifiasm/meta.yml +++ b/modules/hifiasm/meta.yml @@ -45,7 +45,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - raw_unitigs: type: file description: Raw unitigs diff --git a/modules/hisat2/align/functions.nf b/modules/hisat2/align/functions.nf index da9da093..85628ee0 100644 --- a/modules/hisat2/align/functions.nf +++ b/modules/hisat2/align/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/hisat2/align/main.nf b/modules/hisat2/align/main.nf index 17547c91..21eb3c7d 100644 --- a/modules/hisat2/align/main.nf +++ b/modules/hisat2/align/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -28,7 +28,7 @@ process HISAT2_ALIGN { output: tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.log"), emit: summary - path "*.version.txt" , emit: version + path "versions.yml" , emit: version tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq @@ -59,7 +59,10 @@ process HISAT2_ALIGN { $options.args \\ | samtools view -bS -F 4 -F 256 - > ${prefix}.bam - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } else { def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' @@ -87,7 +90,10 @@ process HISAT2_ALIGN { mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz fi - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } } diff --git a/modules/hisat2/align/meta.yml b/modules/hisat2/align/meta.yml index bf5570fd..799f1808 100644 --- a/modules/hisat2/align/meta.yml +++ b/modules/hisat2/align/meta.yml @@ -51,7 +51,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@ntoda03" diff --git a/modules/hisat2/build/functions.nf b/modules/hisat2/build/functions.nf index da9da093..85628ee0 100644 --- a/modules/hisat2/build/functions.nf +++ b/modules/hisat2/build/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/hisat2/build/main.nf b/modules/hisat2/build/main.nf index 3e74b1d4..ae24a6aa 100644 --- a/modules/hisat2/build/main.nf +++ b/modules/hisat2/build/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -28,7 +28,7 @@ process HISAT2_BUILD { output: path "hisat2" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def avail_mem = 0 @@ -65,6 +65,9 @@ process HISAT2_BUILD { $fasta \\ hisat2/${fasta.baseName} - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/hisat2/build/meta.yml b/modules/hisat2/build/meta.yml index 2f34d9d8..1d3fc7e6 100644 --- a/modules/hisat2/build/meta.yml +++ b/modules/hisat2/build/meta.yml @@ -32,7 +32,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - index: type: file description: HISAT2 genome index file diff --git a/modules/hisat2/extractsplicesites/functions.nf b/modules/hisat2/extractsplicesites/functions.nf index da9da093..85628ee0 100644 --- a/modules/hisat2/extractsplicesites/functions.nf +++ b/modules/hisat2/extractsplicesites/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/hisat2/extractsplicesites/main.nf b/modules/hisat2/extractsplicesites/main.nf index d97fdb89..3387cbd1 100644 --- a/modules/hisat2/extractsplicesites/main.nf +++ b/modules/hisat2/extractsplicesites/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,12 +25,15 @@ process HISAT2_EXTRACTSPLICESITES { output: path "*.splice_sites.txt", emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/hisat2/extractsplicesites/meta.yml b/modules/hisat2/extractsplicesites/meta.yml index 228138a8..3befc4dd 100644 --- a/modules/hisat2/extractsplicesites/meta.yml +++ b/modules/hisat2/extractsplicesites/meta.yml @@ -24,7 +24,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - splicesites: type: file description: Splices sites in gtf file diff --git a/modules/hmmer/hmmalign/functions.nf b/modules/hmmer/hmmalign/functions.nf index da9da093..85628ee0 100644 --- a/modules/hmmer/hmmalign/functions.nf +++ b/modules/hmmer/hmmalign/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/hmmer/hmmalign/main.nf b/modules/hmmer/hmmalign/main.nf index 0446707b..a4166fcb 100644 --- a/modules/hmmer/hmmalign/main.nf +++ b/modules/hmmer/hmmalign/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process HMMER_HMMALIGN { output: tuple val(meta), path("*.sthlm.gz"), emit: sthlm - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process HMMER_HMMALIGN { $hmm \\ - | gzip -c > ${meta.id}.sthlm.gz - echo \$(hmmalign -h | grep -o '^# HMMER [0-9.]*') | sed 's/^# HMMER *//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//') + END_VERSIONS """ } diff --git a/modules/hmmer/hmmalign/meta.yml b/modules/hmmer/hmmalign/meta.yml index 563d227d..60020b32 100644 --- a/modules/hmmer/hmmalign/meta.yml +++ b/modules/hmmer/hmmalign/meta.yml @@ -35,7 +35,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - sthlm: type: file description: Multiple alignment in gzipped Stockholm format diff --git a/modules/homer/annotatepeaks/functions.nf b/modules/homer/annotatepeaks/functions.nf index da9da093..85628ee0 100644 --- a/modules/homer/annotatepeaks/functions.nf +++ b/modules/homer/annotatepeaks/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/homer/annotatepeaks/main.nf b/modules/homer/annotatepeaks/main.nf index 22dbb955..198ae1fe 100644 --- a/modules/homer/annotatepeaks/main.nf +++ b/modules/homer/annotatepeaks/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process HOMER_ANNOTATEPEAKS { output: tuple val(meta), path("*annotatePeaks.txt"), emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,6 +41,9 @@ process HOMER_ANNOTATEPEAKS { -cpu $task.cpus \\ > ${prefix}.annotatePeaks.txt - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/homer/annotatepeaks/meta.yml b/modules/homer/annotatepeaks/meta.yml index a22b9618..f311741b 100644 --- a/modules/homer/annotatepeaks/meta.yml +++ b/modules/homer/annotatepeaks/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/homer/findpeaks/functions.nf b/modules/homer/findpeaks/functions.nf index da9da093..85628ee0 100644 --- a/modules/homer/findpeaks/functions.nf +++ b/modules/homer/findpeaks/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/homer/findpeaks/main.nf b/modules/homer/findpeaks/main.nf index 5fcacc1d..fe8399a1 100644 --- a/modules/homer/findpeaks/main.nf +++ b/modules/homer/findpeaks/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] def options = initOptions(params.options) @@ -25,7 +25,7 @@ process HOMER_FINDPEAKS { output: tuple val(meta), path("*peaks.txt"), emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process HOMER_FINDPEAKS { $options.args \\ -o ${prefix}.peaks.txt - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/homer/findpeaks/meta.yml b/modules/homer/findpeaks/meta.yml index d19199d7..51932688 100644 --- a/modules/homer/findpeaks/meta.yml +++ b/modules/homer/findpeaks/meta.yml @@ -32,6 +32,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@EMiller88" diff --git a/modules/homer/maketagdirectory/functions.nf b/modules/homer/maketagdirectory/functions.nf index da9da093..85628ee0 100644 --- a/modules/homer/maketagdirectory/functions.nf +++ b/modules/homer/maketagdirectory/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/homer/maketagdirectory/main.nf b/modules/homer/maketagdirectory/main.nf index e0358bc1..daf0ce60 100644 --- a/modules/homer/maketagdirectory/main.nf +++ b/modules/homer/maketagdirectory/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] def options = initOptions(params.options) @@ -26,7 +26,7 @@ process HOMER_MAKETAGDIRECTORY { output: tuple val(meta), path("tag_dir"), emit: tagdir - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -38,6 +38,9 @@ process HOMER_MAKETAGDIRECTORY { $bed \\ -genome $fasta - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/homer/maketagdirectory/meta.yml b/modules/homer/maketagdirectory/meta.yml index 78dee297..7a35857b 100644 --- a/modules/homer/maketagdirectory/meta.yml +++ b/modules/homer/maketagdirectory/meta.yml @@ -36,6 +36,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@EMiller88" diff --git a/modules/homer/makeucscfile/functions.nf b/modules/homer/makeucscfile/functions.nf index da9da093..85628ee0 100644 --- a/modules/homer/makeucscfile/functions.nf +++ b/modules/homer/makeucscfile/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/homer/makeucscfile/main.nf b/modules/homer/makeucscfile/main.nf index 876d834f..5b23e243 100644 --- a/modules/homer/makeucscfile/main.nf +++ b/modules/homer/makeucscfile/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] def options = initOptions(params.options) @@ -25,7 +25,7 @@ process HOMER_MAKEUCSCFILE { output: tuple val(meta), path("tag_dir/*ucsc.bedGraph.gz"), emit: bedGraph - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process HOMER_MAKEUCSCFILE { -o auto $options.args - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/homer/makeucscfile/meta.yml b/modules/homer/makeucscfile/meta.yml index 891cb295..e63e979a 100644 --- a/modules/homer/makeucscfile/meta.yml +++ b/modules/homer/makeucscfile/meta.yml @@ -33,6 +33,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@EMiller88" diff --git a/modules/iqtree/functions.nf b/modules/iqtree/functions.nf index da9da093..85628ee0 100644 --- a/modules/iqtree/functions.nf +++ b/modules/iqtree/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/iqtree/main.nf b/modules/iqtree/main.nf index 3bd0f3b1..28e07207 100644 --- a/modules/iqtree/main.nf +++ b/modules/iqtree/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process IQTREE { output: path "*.treefile", emit: phylogeny - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process IQTREE { -ntmax $task.cpus \\ -mem $memory \\ - echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version \\([0-9\\.]*\\) .*\$/\\1/' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(iqtree -version 2>&1 | sed 's/^IQ-TREE multicore version \\([0-9\\.]*\\) .*\$/\\1/') + END_VERSIONS """ } diff --git a/modules/iqtree/meta.yml b/modules/iqtree/meta.yml index 19f81b15..426ad0cf 100644 --- a/modules/iqtree/meta.yml +++ b/modules/iqtree/meta.yml @@ -23,7 +23,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - phylogeny: type: file description: A phylogeny in Newick format diff --git a/modules/ivar/consensus/functions.nf b/modules/ivar/consensus/functions.nf index da9da093..85628ee0 100644 --- a/modules/ivar/consensus/functions.nf +++ b/modules/ivar/consensus/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/ivar/consensus/main.nf b/modules/ivar/consensus/main.nf index 1b1019cf..7c4a5b57 100644 --- a/modules/ivar/consensus/main.nf +++ b/modules/ivar/consensus/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process IVAR_CONSENSUS { tuple val(meta), path("*.fa") , emit: fasta tuple val(meta), path("*.qual.txt"), emit: qual tuple val(meta), path("*.mpileup") , optional:true, emit: mpileup - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process IVAR_CONSENSUS { $options.args \\ -p $prefix - echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/ivar/consensus/meta.yml b/modules/ivar/consensus/meta.yml index 913a7660..2a95c51c 100644 --- a/modules/ivar/consensus/meta.yml +++ b/modules/ivar/consensus/meta.yml @@ -45,7 +45,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh" diff --git a/modules/ivar/trim/functions.nf b/modules/ivar/trim/functions.nf index da9da093..85628ee0 100644 --- a/modules/ivar/trim/functions.nf +++ b/modules/ivar/trim/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/ivar/trim/main.nf b/modules/ivar/trim/main.nf index afdc99e4..e9b1e23b 100644 --- a/modules/ivar/trim/main.nf +++ b/modules/ivar/trim/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process IVAR_TRIM { output: tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path('*.log'), emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -38,6 +38,9 @@ process IVAR_TRIM { -p $prefix \\ > ${prefix}.ivar.log - echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/ivar/trim/meta.yml b/modules/ivar/trim/meta.yml index 5791db66..762a9fe9 100644 --- a/modules/ivar/trim/meta.yml +++ b/modules/ivar/trim/meta.yml @@ -45,7 +45,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh" diff --git a/modules/ivar/variants/functions.nf b/modules/ivar/variants/functions.nf index da9da093..85628ee0 100644 --- a/modules/ivar/variants/functions.nf +++ b/modules/ivar/variants/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/ivar/variants/main.nf b/modules/ivar/variants/main.nf index 154f309c..505d72fb 100644 --- a/modules/ivar/variants/main.nf +++ b/modules/ivar/variants/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process IVAR_VARIANTS { output: tuple val(meta), path("*.tsv") , emit: tsv tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -45,6 +45,9 @@ process IVAR_VARIANTS { -r $fasta \\ -p $prefix - echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/ivar/variants/meta.yml b/modules/ivar/variants/meta.yml index 7a5fbbc0..37eb9133 100644 --- a/modules/ivar/variants/meta.yml +++ b/modules/ivar/variants/meta.yml @@ -45,7 +45,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh" diff --git a/modules/kallisto/index/functions.nf b/modules/kallisto/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/kallisto/index/functions.nf +++ b/modules/kallisto/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/kallisto/index/main.nf b/modules/kallisto/index/main.nf index 85eb7f0d..00ae9601 100644 --- a/modules/kallisto/index/main.nf +++ b/modules/kallisto/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process KALLISTO_INDEX { output: path "kallisto" , emit: idx - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process KALLISTO_INDEX { -i kallisto \\ $fasta - echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(kallisto 2>&1 | sed 's/^kallisto //; s/Usage.*\$//') + END_VERSIONS """ } diff --git a/modules/kallisto/index/meta.yml b/modules/kallisto/index/meta.yml index 24b44b0b..ba4855b0 100644 --- a/modules/kallisto/index/meta.yml +++ b/modules/kallisto/index/meta.yml @@ -21,7 +21,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - idx: type: index description: Kallisto genome index diff --git a/modules/kallistobustools/count/functions.nf b/modules/kallistobustools/count/functions.nf index da9da093..85628ee0 100644 --- a/modules/kallistobustools/count/functions.nf +++ b/modules/kallistobustools/count/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/kallistobustools/count/main.nf b/modules/kallistobustools/count/main.nf index cb561a9d..309bd57c 100644 --- a/modules/kallistobustools/count/main.nf +++ b/modules/kallistobustools/count/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -29,7 +29,7 @@ process KALLISTOBUSTOOLS_COUNT { output: tuple val(meta), path ("*.count"), emit: count - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -51,6 +51,9 @@ process KALLISTOBUSTOOLS_COUNT { ${reads[0]} \\ ${reads[1]} - echo \$(kb 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//') + END_VERSIONS """ } diff --git a/modules/kallistobustools/count/meta.yml b/modules/kallistobustools/count/meta.yml index 688dfdef..41cf91a0 100644 --- a/modules/kallistobustools/count/meta.yml +++ b/modules/kallistobustools/count/meta.yml @@ -61,7 +61,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@flowuenne" diff --git a/modules/kallistobustools/ref/functions.nf b/modules/kallistobustools/ref/functions.nf index da9da093..85628ee0 100644 --- a/modules/kallistobustools/ref/functions.nf +++ b/modules/kallistobustools/ref/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/kallistobustools/ref/main.nf b/modules/kallistobustools/ref/main.nf index 93935696..bc9b32f5 100644 --- a/modules/kallistobustools/ref/main.nf +++ b/modules/kallistobustools/ref/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process KALLISTOBUSTOOLS_REF { val workflow output: - path "*.version.txt" , emit: version + path "versions.yml" , emit: version path "kb_ref_out.idx" , emit: index path "t2g.txt" , emit: t2g path "cdna.fa" , emit: cdna @@ -45,7 +45,10 @@ process KALLISTOBUSTOOLS_REF { $fasta \\ $gtf - echo \$(kb 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//') + END_VERSIONS """ } else { """ @@ -61,7 +64,10 @@ process KALLISTOBUSTOOLS_REF { $fasta \\ $gtf - echo \$(kb 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//') + END_VERSIONS """ } } diff --git a/modules/kallistobustools/ref/meta.yml b/modules/kallistobustools/ref/meta.yml index c2a85b37..b9f50f20 100644 --- a/modules/kallistobustools/ref/meta.yml +++ b/modules/kallistobustools/ref/meta.yml @@ -30,7 +30,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - kb_ref_idx: type: file description: Index file from kb ref. diff --git a/modules/kleborate/functions.nf b/modules/kleborate/functions.nf index da9da093..85628ee0 100644 --- a/modules/kleborate/functions.nf +++ b/modules/kleborate/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/kleborate/main.nf b/modules/kleborate/main.nf index ef7eab23..0079071f 100644 --- a/modules/kleborate/main.nf +++ b/modules/kleborate/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process KLEBORATE { output: tuple val(meta), path("*.txt"), emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process KLEBORATE { --outfile ${prefix}.results.txt \\ --assemblies *.fasta - echo \$(kleborate -v 2>&1) | sed 's/kleborate //;' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(kleborate -v 2>&1 | sed 's/kleborate //;') + END_VERSIONS """ } diff --git a/modules/kleborate/meta.yml b/modules/kleborate/meta.yml index 19643033..0394a626 100644 --- a/modules/kleborate/meta.yml +++ b/modules/kleborate/meta.yml @@ -32,7 +32,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - txt: type: file description: Result file generated after screening diff --git a/modules/kraken2/kraken2/functions.nf b/modules/kraken2/kraken2/functions.nf index da9da093..85628ee0 100644 --- a/modules/kraken2/kraken2/functions.nf +++ b/modules/kraken2/kraken2/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/kraken2/kraken2/main.nf b/modules/kraken2/kraken2/main.nf index ea0b72fd..9a01389a 100644 --- a/modules/kraken2/kraken2/main.nf +++ b/modules/kraken2/kraken2/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process KRAKEN2_KRAKEN2 { tuple val(meta), path('*classified*') , emit: classified tuple val(meta), path('*unclassified*'), emit: unclassified tuple val(meta), path('*report.txt') , emit: txt - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -48,6 +48,9 @@ process KRAKEN2_KRAKEN2 { pigz -p $task.cpus *.fastq - echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(kraken2 --version 2>&1 | sed 's/^.*Kraken version //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/kraken2/kraken2/meta.yml b/modules/kraken2/kraken2/meta.yml index cb1ec0de..3996fbc0 100644 --- a/modules/kraken2/kraken2/meta.yml +++ b/modules/kraken2/kraken2/meta.yml @@ -53,7 +53,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/last/dotplot/functions.nf b/modules/last/dotplot/functions.nf index da9da093..85628ee0 100644 --- a/modules/last/dotplot/functions.nf +++ b/modules/last/dotplot/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/last/dotplot/main.nf b/modules/last/dotplot/main.nf index 3644a18e..ca30bbff 100644 --- a/modules/last/dotplot/main.nf +++ b/modules/last/dotplot/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process LAST_DOTPLOT { output: tuple val(meta), path("*.gif"), optional:true, emit: gif tuple val(meta), path("*.png"), optional:true, emit: png - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process LAST_DOTPLOT { $prefix.$format # last-dotplot has no --version option so let's use lastal from the same suite - lastal --version | sed 's/lastal //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lastal --version | sed 's/lastal //') + END_VERSIONS """ } diff --git a/modules/last/dotplot/meta.yml b/modules/last/dotplot/meta.yml index ab57dab7..fa092b4c 100644 --- a/modules/last/dotplot/meta.yml +++ b/modules/last/dotplot/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@charles-plessy" diff --git a/modules/last/lastal/functions.nf b/modules/last/lastal/functions.nf index da9da093..85628ee0 100644 --- a/modules/last/lastal/functions.nf +++ b/modules/last/lastal/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/last/lastal/main.nf b/modules/last/lastal/main.nf index e42653cc..3d6518a4 100644 --- a/modules/last/lastal/main.nf +++ b/modules/last/lastal/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process LAST_LASTAL { output: tuple val(meta), path("*.maf.gz"), emit: maf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process LAST_LASTAL { # gzip needs --no-name otherwise it puts a timestamp in the file, # which makes its checksum non-reproducible. - echo \$(lastal --version 2>&1) | sed 's/lastal //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lastal --version 2>&1 | sed 's/lastal //') + END_VERSIONS """ } diff --git a/modules/last/lastal/meta.yml b/modules/last/lastal/meta.yml index 2237c75a..1f8fde9c 100644 --- a/modules/last/lastal/meta.yml +++ b/modules/last/lastal/meta.yml @@ -42,7 +42,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - maf: type: file description: Gzipped MAF (Multiple Alignment Format) file diff --git a/modules/last/lastdb/functions.nf b/modules/last/lastdb/functions.nf index da9da093..85628ee0 100644 --- a/modules/last/lastdb/functions.nf +++ b/modules/last/lastdb/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/last/lastdb/main.nf b/modules/last/lastdb/main.nf index a8cd4921..ac552e7d 100644 --- a/modules/last/lastdb/main.nf +++ b/modules/last/lastdb/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process LAST_LASTDB { output: tuple val(meta), path("lastdb"), emit: index - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process LAST_LASTDB { lastdb/${prefix} \\ $fastx - echo \$(lastdb --version 2>&1) | sed 's/lastdb //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lastdb --version 2>&1 | sed 's/lastdb //') + END_VERSIONS """ } diff --git a/modules/last/lastdb/meta.yml b/modules/last/lastdb/meta.yml index 64e4d3e3..cddbc29c 100644 --- a/modules/last/lastdb/meta.yml +++ b/modules/last/lastdb/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - index: type: directory description: directory containing the files of the LAST index diff --git a/modules/last/mafconvert/functions.nf b/modules/last/mafconvert/functions.nf index da9da093..85628ee0 100644 --- a/modules/last/mafconvert/functions.nf +++ b/modules/last/mafconvert/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/last/mafconvert/main.nf b/modules/last/mafconvert/main.nf index eea53dd1..e112cbd8 100644 --- a/modules/last/mafconvert/main.nf +++ b/modules/last/mafconvert/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -32,7 +32,7 @@ process LAST_MAFCONVERT { tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process LAST_MAFCONVERT { > ${prefix}.${format}.gz # maf-convert has no --version option but lastdb (part of the same package) has. - echo \$(lastdb --version 2>&1) | sed 's/lastdb //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lastdb --version 2>&1 | sed 's/lastdb //') + END_VERSIONS """ } diff --git a/modules/last/mafconvert/meta.yml b/modules/last/mafconvert/meta.yml index 0ab87457..f0912ccd 100644 --- a/modules/last/mafconvert/meta.yml +++ b/modules/last/mafconvert/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - axt_gz: type: file description: Gzipped pairwise alignment in Axt (Blastz) format (optional) diff --git a/modules/last/mafswap/functions.nf b/modules/last/mafswap/functions.nf index da9da093..85628ee0 100644 --- a/modules/last/mafswap/functions.nf +++ b/modules/last/mafswap/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/last/mafswap/main.nf b/modules/last/mafswap/main.nf index 03292c81..f597693c 100644 --- a/modules/last/mafswap/main.nf +++ b/modules/last/mafswap/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process LAST_MAFSWAP { output: tuple val(meta), path("*.maf.gz"), emit: maf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -32,6 +32,9 @@ process LAST_MAFSWAP { maf-swap $options.args $maf | gzip --no-name > ${prefix}.swapped.maf.gz # maf-swap has no --version option but lastdb, part of the same package, has. - echo \$(lastdb --version 2>&1) | sed 's/lastdb //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lastdb --version 2>&1 | sed 's/lastdb //') + END_VERSIONS """ } diff --git a/modules/last/mafswap/meta.yml b/modules/last/mafswap/meta.yml index eb35a46c..8821ab47 100644 --- a/modules/last/mafswap/meta.yml +++ b/modules/last/mafswap/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@charles-plessy" diff --git a/modules/last/postmask/functions.nf b/modules/last/postmask/functions.nf index da9da093..85628ee0 100644 --- a/modules/last/postmask/functions.nf +++ b/modules/last/postmask/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/last/postmask/main.nf b/modules/last/postmask/main.nf index 677b23f6..d3fa02e3 100644 --- a/modules/last/postmask/main.nf +++ b/modules/last/postmask/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process LAST_POSTMASK { output: tuple val(meta), path("*.maf.gz"), emit: maf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process LAST_POSTMASK { last-postmask $options.args $maf | gzip --no-name > ${prefix}.maf.gz # last-postmask does not have a --version option - echo \$(lastal --version 2>&1) | sed 's/lastal //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lastal --version 2>&1 | sed 's/lastal //') + END_VERSIONS """ } diff --git a/modules/last/postmask/meta.yml b/modules/last/postmask/meta.yml index 45eaa2b9..d3a184eb 100644 --- a/modules/last/postmask/meta.yml +++ b/modules/last/postmask/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@charles-plessy" diff --git a/modules/last/split/functions.nf b/modules/last/split/functions.nf index da9da093..85628ee0 100644 --- a/modules/last/split/functions.nf +++ b/modules/last/split/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/last/split/main.nf b/modules/last/split/main.nf index a6fe1dda..78d59ed4 100644 --- a/modules/last/split/main.nf +++ b/modules/last/split/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process LAST_SPLIT { output: tuple val(meta), path("*.maf.gz"), emit: maf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -31,6 +31,9 @@ process LAST_SPLIT { """ zcat < $maf | last-split $options.args | gzip --no-name > ${prefix}.maf.gz - echo \$(last-split --version 2>&1) | sed 's/last-split //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(last-split --version 2>&1 | sed 's/last-split //') + END_VERSIONS """ } diff --git a/modules/last/split/meta.yml b/modules/last/split/meta.yml index 73f37784..7b11bcd5 100644 --- a/modules/last/split/meta.yml +++ b/modules/last/split/meta.yml @@ -35,7 +35,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - maf: type: file description: Multiple Aligment Format (MAF) file, compressed with gzip diff --git a/modules/last/train/functions.nf b/modules/last/train/functions.nf index da9da093..85628ee0 100644 --- a/modules/last/train/functions.nf +++ b/modules/last/train/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/last/train/main.nf b/modules/last/train/main.nf index cc1fa544..39728ced 100644 --- a/modules/last/train/main.nf +++ b/modules/last/train/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process LAST_TRAIN { output: tuple val(meta), path("*.par"), emit: param_file - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process LAST_TRAIN { $fastx \\ > ${prefix}.\$INDEX_NAME.par - lastdb --version | sed 's/lastdb //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lastdb --version | sed 's/lastdb //') + END_VERSIONS """ } diff --git a/modules/last/train/meta.yml b/modules/last/train/meta.yml index 5796b764..820e4bc8 100644 --- a/modules/last/train/meta.yml +++ b/modules/last/train/meta.yml @@ -38,7 +38,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - param_file: type: file description: Trained parameter file diff --git a/modules/lib/functions.nf b/modules/lib/functions.nf index da9da093..85628ee0 100644 --- a/modules/lib/functions.nf +++ b/modules/lib/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/lofreq/call/functions.nf b/modules/lofreq/call/functions.nf index da9da093..85628ee0 100644 --- a/modules/lofreq/call/functions.nf +++ b/modules/lofreq/call/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/lofreq/call/main.nf b/modules/lofreq/call/main.nf index d342c929..b205f041 100644 --- a/modules/lofreq/call/main.nf +++ b/modules/lofreq/call/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process LOFREQ_CALL { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process LOFREQ_CALL { -o ${prefix}.vcf.gz \\ $bam - echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//') + END_VERSIONS """ } diff --git a/modules/lofreq/call/meta.yml b/modules/lofreq/call/meta.yml index f14115d2..16d23cd9 100644 --- a/modules/lofreq/call/meta.yml +++ b/modules/lofreq/call/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - vcf: type: file description: VCF output file diff --git a/modules/lofreq/callparallel/functions.nf b/modules/lofreq/callparallel/functions.nf index da9da093..85628ee0 100644 --- a/modules/lofreq/callparallel/functions.nf +++ b/modules/lofreq/callparallel/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/lofreq/callparallel/main.nf b/modules/lofreq/callparallel/main.nf index 4392c700..2bea68f2 100644 --- a/modules/lofreq/callparallel/main.nf +++ b/modules/lofreq/callparallel/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process LOFREQ_CALLPARALLEL { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process LOFREQ_CALLPARALLEL { -o ${prefix}.vcf.gz \\ $bam - echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//') + END_VERSIONS """ } diff --git a/modules/lofreq/callparallel/meta.yml b/modules/lofreq/callparallel/meta.yml index 3154f412..15257180 100644 --- a/modules/lofreq/callparallel/meta.yml +++ b/modules/lofreq/callparallel/meta.yml @@ -43,7 +43,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - vcf: type: file description: Predicted variants file diff --git a/modules/lofreq/filter/functions.nf b/modules/lofreq/filter/functions.nf index da9da093..85628ee0 100644 --- a/modules/lofreq/filter/functions.nf +++ b/modules/lofreq/filter/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/lofreq/filter/main.nf b/modules/lofreq/filter/main.nf index a2b53f08..693cef23 100644 --- a/modules/lofreq/filter/main.nf +++ b/modules/lofreq/filter/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process LOFREQ_FILTER { output: tuple val(meta), path("*.gz"), emit: vcf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process LOFREQ_FILTER { -i $vcf \\ -o ${prefix}.vcf.gz - echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//') + END_VERSIONS """ } diff --git a/modules/lofreq/filter/meta.yml b/modules/lofreq/filter/meta.yml index 9de18d4d..9aa92da7 100644 --- a/modules/lofreq/filter/meta.yml +++ b/modules/lofreq/filter/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - vcf: type: file description: VCF filtered output file diff --git a/modules/lofreq/indelqual/functions.nf b/modules/lofreq/indelqual/functions.nf index da9da093..85628ee0 100644 --- a/modules/lofreq/indelqual/functions.nf +++ b/modules/lofreq/indelqual/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/lofreq/indelqual/main.nf b/modules/lofreq/indelqual/main.nf index befd8d7a..89c79c39 100644 --- a/modules/lofreq/indelqual/main.nf +++ b/modules/lofreq/indelqual/main.nf @@ -1,4 +1,4 @@ -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process LOFREQ_INDELQUAL { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process LOFREQ_INDELQUAL { -o ${prefix}.bam \\ $bam - echo \$(lofreq version 2>&1) | sed 's/^.*lofreq //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^.*lofreq //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/lofreq/indelqual/meta.yml b/modules/lofreq/indelqual/meta.yml index 294cf17d..34f296d7 100644 --- a/modules/lofreq/indelqual/meta.yml +++ b/modules/lofreq/indelqual/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: BAM file with indel qualities inserted into it diff --git a/modules/macs2/callpeak/functions.nf b/modules/macs2/callpeak/functions.nf index da9da093..85628ee0 100644 --- a/modules/macs2/callpeak/functions.nf +++ b/modules/macs2/callpeak/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/macs2/callpeak/main.nf b/modules/macs2/callpeak/main.nf index 67d686c6..4fcd6b05 100644 --- a/modules/macs2/callpeak/main.nf +++ b/modules/macs2/callpeak/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process MACS2_CALLPEAK { output: tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak tuple val(meta), path("*.xls") , emit: xls - path "*.version.txt" , emit: version + path "versions.yml" , emit: version tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped tuple val(meta), path("*.bed") , optional:true, emit: bed @@ -46,6 +46,9 @@ process MACS2_CALLPEAK { --treatment $ipbam \\ $control - macs2 --version | sed -e "s/macs2 //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(macs2 --version | sed -e "s/macs2 //g") + END_VERSIONS """ } diff --git a/modules/malt/build/functions.nf b/modules/malt/build/functions.nf index da9da093..85628ee0 100644 --- a/modules/malt/build/functions.nf +++ b/modules/malt/build/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/malt/build/main.nf b/modules/malt/build/main.nf index a7e3751b..3b494c0c 100644 --- a/modules/malt/build/main.nf +++ b/modules/malt/build/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process MALT_BUILD { output: path "malt_index/" , emit: index - path "*.version.txt" , emit: version + path "versions.yml" , emit: version path "malt-build.log", emit: log script: @@ -51,6 +51,9 @@ process MALT_BUILD { $options.args \\ -mdb ${map_db}/*.db |&tee malt-build.log - malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2 > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2) + END_VERSIONS """ } diff --git a/modules/malt/build/meta.yml b/modules/malt/build/meta.yml index 5ace4d29..f1668b94 100644 --- a/modules/malt/build/meta.yml +++ b/modules/malt/build/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - index: type: directory description: Directory containing MALT database index directory diff --git a/modules/malt/run/functions.nf b/modules/malt/run/functions.nf index da9da093..85628ee0 100644 --- a/modules/malt/run/functions.nf +++ b/modules/malt/run/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/malt/run/main.nf b/modules/malt/run/main.nf index 8add081c..689dabf4 100644 --- a/modules/malt/run/main.nf +++ b/modules/malt/run/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process MALT_RUN { path "*.rma6" , emit: rma6 path "*.{tab,text,sam}", optional:true, emit: alignments path "*.log" , emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -49,6 +49,9 @@ process MALT_RUN { -m $mode \\ --index $index/ |&tee malt-run.log - echo \$(malt-run --help 2>&1) | grep -o 'version.* ' | cut -f 1 -d ',' | cut -f2 -d ' ' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(malt-run --help 2>&1 | grep -o 'version.* ' | cut -f 1 -d ',' | cut -f2 -d ' ') + END_VERSIONS """ } diff --git a/modules/malt/run/meta.yml b/modules/malt/run/meta.yml index 30421a48..3ad78622 100644 --- a/modules/malt/run/meta.yml +++ b/modules/malt/run/meta.yml @@ -35,7 +35,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - rma6: type: file description: MEGAN6 RMA6 file diff --git a/modules/maltextract/functions.nf b/modules/maltextract/functions.nf index da9da093..85628ee0 100644 --- a/modules/maltextract/functions.nf +++ b/modules/maltextract/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/maltextract/main.nf b/modules/maltextract/main.nf index d7402cb8..426a9fc3 100644 --- a/modules/maltextract/main.nf +++ b/modules/maltextract/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process MALTEXTRACT { output: path "results" , emit: results - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process MALTEXTRACT { -o results/ \\ $options.args - echo \$(MaltExtract --help | head -n 2 | tail -n 1) | sed 's/MaltExtract version//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//') + END_VERSIONS """ } diff --git a/modules/maltextract/meta.yml b/modules/maltextract/meta.yml index 3cb20fa2..29271753 100644 --- a/modules/maltextract/meta.yml +++ b/modules/maltextract/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - results: type: directory description: Directory containing MaltExtract text results files diff --git a/modules/mash/sketch/functions.nf b/modules/mash/sketch/functions.nf index da9da093..85628ee0 100644 --- a/modules/mash/sketch/functions.nf +++ b/modules/mash/sketch/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/mash/sketch/main.nf b/modules/mash/sketch/main.nf index 3cc7e199..ed018b1a 100644 --- a/modules/mash/sketch/main.nf +++ b/modules/mash/sketch/main.nf @@ -1,4 +1,4 @@ -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -22,7 +22,7 @@ process MASH_SKETCH { output: tuple val(meta), path("*.msh") , emit: mash tuple val(meta), path("*.mash_stats") , emit: stats - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process MASH_SKETCH { -o ${prefix} \\ -r $reads \\ 2> ${prefix}.mash_stats - echo \$(mash --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(mash --version 2>&1) + END_VERSIONS """ } diff --git a/modules/metaphlan3/functions.nf b/modules/metaphlan3/functions.nf index da9da093..85628ee0 100644 --- a/modules/metaphlan3/functions.nf +++ b/modules/metaphlan3/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/metaphlan3/main.nf b/modules/metaphlan3/main.nf index 6c75c2a0..8893c2ab 100644 --- a/modules/metaphlan3/main.nf +++ b/modules/metaphlan3/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process METAPHLAN3 { tuple val(meta), path("*_profile.txt") , emit: profile tuple val(meta), path("*.biom") , emit: biom tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -45,6 +45,9 @@ process METAPHLAN3 { --bowtie2db ${metaphlan_db} \\ --biom ${prefix}.biom \\ --output_file ${prefix}_profile.txt - echo \$(metaphlan --version 2>&1) | awk '{print \$3}' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(metaphlan --version 2>&1 | awk '{print \$3}') + END_VERSIONS """ } diff --git a/modules/metaphlan3/meta.yml b/modules/metaphlan3/meta.yml index e0d54d88..d9f9f520 100644 --- a/modules/metaphlan3/meta.yml +++ b/modules/metaphlan3/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - profile: type: file description: Tab-separated output file of the predicted taxon relative abundances diff --git a/modules/methyldackel/extract/functions.nf b/modules/methyldackel/extract/functions.nf index da9da093..85628ee0 100644 --- a/modules/methyldackel/extract/functions.nf +++ b/modules/methyldackel/extract/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/methyldackel/extract/main.nf b/modules/methyldackel/extract/main.nf index 4c7da3f4..149f4aa0 100644 --- a/modules/methyldackel/extract/main.nf +++ b/modules/methyldackel/extract/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process METHYLDACKEL_EXTRACT { output: tuple val(meta), path("*.bedGraph"), emit: bedgraph - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process METHYLDACKEL_EXTRACT { $fasta \\ $bam - echo \$(MethylDackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(MethylDackel --version 2>&1 | cut -f1 -d" ") + END_VERSIONS """ } diff --git a/modules/methyldackel/extract/meta.yml b/modules/methyldackel/extract/meta.yml index 525ddebe..7219bb81 100644 --- a/modules/methyldackel/extract/meta.yml +++ b/modules/methyldackel/extract/meta.yml @@ -52,6 +52,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/methyldackel/mbias/functions.nf b/modules/methyldackel/mbias/functions.nf index da9da093..85628ee0 100644 --- a/modules/methyldackel/mbias/functions.nf +++ b/modules/methyldackel/mbias/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/methyldackel/mbias/main.nf b/modules/methyldackel/mbias/main.nf index 7c18197f..9fa39b82 100644 --- a/modules/methyldackel/mbias/main.nf +++ b/modules/methyldackel/mbias/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process METHYLDACKEL_MBIAS { output: tuple val(meta), path("*.mbias.txt"), emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process METHYLDACKEL_MBIAS { --txt \\ > ${prefix}.mbias.txt - echo \$(MethylDackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(MethylDackel --version 2>&1 | cut -f1 -d" ") + END_VERSIONS """ } diff --git a/modules/methyldackel/mbias/meta.yml b/modules/methyldackel/mbias/meta.yml index e41d0208..a6f58d09 100644 --- a/modules/methyldackel/mbias/meta.yml +++ b/modules/methyldackel/mbias/meta.yml @@ -53,6 +53,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/minia/functions.nf b/modules/minia/functions.nf index da9da093..85628ee0 100644 --- a/modules/minia/functions.nf +++ b/modules/minia/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/minia/main.nf b/modules/minia/main.nf index 9ae79ede..b7aa9272 100644 --- a/modules/minia/main.nf +++ b/modules/minia/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process MINIA { tuple val(meta), path('*.contigs.fa'), emit: contigs tuple val(meta), path('*.unitigs.fa'), emit: unitigs tuple val(meta), path('*.h5') , emit: h5 - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -38,6 +38,9 @@ process MINIA { -in input_files.txt \\ -out $prefix - echo \$(minia --version 2>&1) | sed 's/^.*Minia version //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(minia --version 2>&1 | sed 's/^.*Minia version //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/minia/meta.yml b/modules/minia/meta.yml index d3a76be8..638cc3ad 100644 --- a/modules/minia/meta.yml +++ b/modules/minia/meta.yml @@ -40,7 +40,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/minimap2/align/functions.nf b/modules/minimap2/align/functions.nf index da9da093..85628ee0 100644 --- a/modules/minimap2/align/functions.nf +++ b/modules/minimap2/align/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf index ec5f6a07..d0ff9c0f 100644 --- a/modules/minimap2/align/main.nf +++ b/modules/minimap2/align/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process MINIMAP2_ALIGN { output: tuple val(meta), path("*.paf"), emit: paf - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -38,6 +38,9 @@ process MINIMAP2_ALIGN { $input_reads \\ > ${prefix}.paf - echo \$(minimap2 --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(minimap2 --version 2>&1) + END_VERSIONS """ } diff --git a/modules/minimap2/align/meta.yml b/modules/minimap2/align/meta.yml index 3c741b16..1cb20473 100644 --- a/modules/minimap2/align/meta.yml +++ b/modules/minimap2/align/meta.yml @@ -41,6 +41,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@heuermh" diff --git a/modules/minimap2/index/functions.nf b/modules/minimap2/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/minimap2/index/functions.nf +++ b/modules/minimap2/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/minimap2/index/main.nf b/modules/minimap2/index/main.nf index e143bd62..cfc40417 100644 --- a/modules/minimap2/index/main.nf +++ b/modules/minimap2/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -22,7 +22,7 @@ process MINIMAP2_INDEX { output: path "*.mmi" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process MINIMAP2_INDEX { $options.args \\ $fasta - echo \$(minimap2 --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(minimap2 --version 2>&1) + END_VERSIONS """ } diff --git a/modules/minimap2/index/meta.yml b/modules/minimap2/index/meta.yml index 065e5c32..c1c43c70 100644 --- a/modules/minimap2/index/meta.yml +++ b/modules/minimap2/index/meta.yml @@ -23,7 +23,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/mosdepth/functions.nf b/modules/mosdepth/functions.nf index da9da093..85628ee0 100644 --- a/modules/mosdepth/functions.nf +++ b/modules/mosdepth/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index 6beea37a..c21ea2a8 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -31,7 +31,7 @@ process MOSDEPTH { tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -43,6 +43,9 @@ process MOSDEPTH { $options.args \\ $prefix \\ $bam - echo \$(mosdepth --version 2>&1) | sed 's/^.*mosdepth //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/mosdepth/meta.yml b/modules/mosdepth/meta.yml index d96e474f..4c0be86c 100644 --- a/modules/mosdepth/meta.yml +++ b/modules/mosdepth/meta.yml @@ -70,7 +70,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/msisensor/msi/functions.nf b/modules/msisensor/msi/functions.nf index da9da093..85628ee0 100644 --- a/modules/msisensor/msi/functions.nf +++ b/modules/msisensor/msi/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/msisensor/msi/main.nf b/modules/msisensor/msi/main.nf index b4a0eb3c..41f79b3a 100644 --- a/modules/msisensor/msi/main.nf +++ b/modules/msisensor/msi/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process MSISENSOR_MSI { tuple val(meta), path("${prefix}_dis") , emit: output_dis tuple val(meta), path("${prefix}_germline"), emit: output_germline tuple val(meta), path("${prefix}_somatic") , emit: output_somatic - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -40,6 +40,9 @@ process MSISENSOR_MSI { -o $prefix \\ $options.args - echo \$(msisensor 2>&1) | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(msisensor 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p') + END_VERSIONS """ } diff --git a/modules/msisensor/msi/meta.yml b/modules/msisensor/msi/meta.yml index 214f90e6..c01f74e0 100644 --- a/modules/msisensor/msi/meta.yml +++ b/modules/msisensor/msi/meta.yml @@ -48,7 +48,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - txt: type: file description: MSIsensor MSI final report file diff --git a/modules/msisensor/scan/functions.nf b/modules/msisensor/scan/functions.nf index da9da093..85628ee0 100644 --- a/modules/msisensor/scan/functions.nf +++ b/modules/msisensor/scan/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/msisensor/scan/main.nf b/modules/msisensor/scan/main.nf index 57ebeb28..198657ae 100644 --- a/modules/msisensor/scan/main.nf +++ b/modules/msisensor/scan/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process MSISENSOR_SCAN { output: tuple (val(meta), path("*.tab"), emit: txt) - path ("*.version.txt" , emit: version) + path ("versions.yml" , emit: version) script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process MSISENSOR_SCAN { -o ${prefix}.msisensor_scan.tab \\ $options.args - echo \$(msisensor 2>&1) | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(msisensor 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p') + END_VERSIONS """ } diff --git a/modules/msisensor/scan/meta.yml b/modules/msisensor/scan/meta.yml index 2e4f8f18..940b53a5 100644 --- a/modules/msisensor/scan/meta.yml +++ b/modules/msisensor/scan/meta.yml @@ -32,7 +32,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - txt: type: file description: MSIsensor scan output file of homopolymers & minisatellites diff --git a/modules/muscle/functions.nf b/modules/muscle/functions.nf index da9da093..85628ee0 100644 --- a/modules/muscle/functions.nf +++ b/modules/muscle/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/muscle/main.nf b/modules/muscle/main.nf index 9f4747a4..ef9bf484 100644 --- a/modules/muscle/main.nf +++ b/modules/muscle/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -30,7 +30,7 @@ process MUSCLE { tuple val(meta), path("*.msf") , optional: true, emit: msf tuple val(meta), path("*.tree"), optional: true, emit: tree path "*.log" , emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -55,6 +55,9 @@ process MUSCLE { $html_out \\ $tree_out \\ -loga muscle_msa.log - muscle -version | sed 's/^MUSCLE v//; s/by.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(muscle -version | sed 's/^MUSCLE v//; s/by.*\$//') + END_VERSIONS """ } diff --git a/modules/muscle/meta.yml b/modules/muscle/meta.yml index e0eb5289..845a8284 100644 --- a/modules/muscle/meta.yml +++ b/modules/muscle/meta.yml @@ -51,6 +51,6 @@ output: - version: type: file description: File containing MUSCLE software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@MGordon" diff --git a/modules/nanolyse/functions.nf b/modules/nanolyse/functions.nf index da9da093..85628ee0 100644 --- a/modules/nanolyse/functions.nf +++ b/modules/nanolyse/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/nanolyse/main.nf b/modules/nanolyse/main.nf index 0abad6cb..84cf579a 100644 --- a/modules/nanolyse/main.nf +++ b/modules/nanolyse/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process NANOLYSE { output: tuple val(meta), path("*.fastq.gz"), emit: fastq path "*.log" , emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process NANOLYSE { gunzip -c $fastq | NanoLyse -r $fasta | gzip > ${prefix}.fastq.gz mv NanoLyse.log ${prefix}.nanolyse.log - echo \$(NanoLyse --version 2>&1) | sed -e "s/NanoLyse //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(NanoLyse --version 2>&1 | sed -e "s/NanoLyse //g") + END_VERSIONS """ } diff --git a/modules/nanolyse/meta.yml b/modules/nanolyse/meta.yml index aae299da..2411d33d 100644 --- a/modules/nanolyse/meta.yml +++ b/modules/nanolyse/meta.yml @@ -41,6 +41,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@yuukiiwa" diff --git a/modules/nanoplot/functions.nf b/modules/nanoplot/functions.nf index da9da093..85628ee0 100644 --- a/modules/nanoplot/functions.nf +++ b/modules/nanoplot/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/nanoplot/main.nf b/modules/nanoplot/main.nf index f5fffe13..86b300f5 100644 --- a/modules/nanoplot/main.nf +++ b/modules/nanoplot/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process NANOPLOT { tuple val(meta), path("*.png") , emit: png tuple val(meta), path("*.txt") , emit: txt tuple val(meta), path("*.log") , emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process NANOPLOT { $options.args \\ -t $task.cpus \\ $input_file - echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(NanoPlot --version 2>&1 | sed 's/^.*NanoPlot //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/nanoplot/meta.yml b/modules/nanoplot/meta.yml index f1d94312..cf897eb9 100644 --- a/modules/nanoplot/meta.yml +++ b/modules/nanoplot/meta.yml @@ -52,7 +52,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@yuukiiwa" diff --git a/modules/nextclade/functions.nf b/modules/nextclade/functions.nf index da9da093..85628ee0 100755 --- a/modules/nextclade/functions.nf +++ b/modules/nextclade/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/nextclade/main.nf b/modules/nextclade/main.nf index 8319f6b1..fabf4520 100755 --- a/modules/nextclade/main.nf +++ b/modules/nextclade/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process NEXTCLADE { tuple val(meta), path("${prefix}.tree.json") , emit: json_tree tuple val(meta), path("${prefix}.tsv") , emit: tsv tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -43,6 +43,9 @@ process NEXTCLADE { --output-tsv-clades-only ${prefix}.clades.tsv \\ --output-tree ${prefix}.tree.json - echo \$(nextclade --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(nextclade --version 2>&1) + END_VERSIONS """ } diff --git a/modules/nextclade/meta.yml b/modules/nextclade/meta.yml index d321e08f..730b0fa4 100755 --- a/modules/nextclade/meta.yml +++ b/modules/nextclade/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - csv: type: file description: CSV file containing nextclade results diff --git a/modules/optitype/functions.nf b/modules/optitype/functions.nf index da9da093..85628ee0 100644 --- a/modules/optitype/functions.nf +++ b/modules/optitype/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/optitype/main.nf b/modules/optitype/main.nf index 15e26c95..4f136d7c 100644 --- a/modules/optitype/main.nf +++ b/modules/optitype/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process OPTITYPE { output: tuple val(meta), path("${prefix}"), emit: output - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -48,6 +48,9 @@ process OPTITYPE { OptiTypePipeline.py -i ${bam} -c config.ini --${meta.seq_type} $options.args --prefix $prefix --outdir $prefix #Couldn't find a nicer way of doing this - cat \$(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(cat \$(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g") + END_VERSIONS """ } diff --git a/modules/optitype/meta.yml b/modules/optitype/meta.yml index 734c4f77..02e5cec1 100644 --- a/modules/optitype/meta.yml +++ b/modules/optitype/meta.yml @@ -32,7 +32,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - output: type: file description: OptiType Results Folder diff --git a/modules/pairix/functions.nf b/modules/pairix/functions.nf index da9da093..85628ee0 100644 --- a/modules/pairix/functions.nf +++ b/modules/pairix/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pairix/main.nf b/modules/pairix/main.nf index ff1b8520..684ea7e6 100644 --- a/modules/pairix/main.nf +++ b/modules/pairix/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process PAIRIX { output: tuple val(meta), path(pair), path("*.px2"), emit: index - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -32,6 +32,9 @@ process PAIRIX { $options.args \\ $pair - echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pairix --help 2>&1 | sed 's/^.*Version: //; s/Usage.*\$//') + END_VERSIONS """ } diff --git a/modules/pairix/meta.yml b/modules/pairix/meta.yml index b0ac1b15..3c43541a 100644 --- a/modules/pairix/meta.yml +++ b/modules/pairix/meta.yml @@ -32,7 +32,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - index: type: file description: pair index file diff --git a/modules/pairtools/dedup/functions.nf b/modules/pairtools/dedup/functions.nf index da9da093..85628ee0 100644 --- a/modules/pairtools/dedup/functions.nf +++ b/modules/pairtools/dedup/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pairtools/dedup/main.nf b/modules/pairtools/dedup/main.nf index 07c81c6c..5b901a77 100644 --- a/modules/pairtools/dedup/main.nf +++ b/modules/pairtools/dedup/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process PAIRTOOLS_DEDUP { output: tuple val(meta), path("*.pairs.gz") , emit: pairs tuple val(meta), path("*.pairs.stat"), emit: stat - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process PAIRTOOLS_DEDUP { --output-stats ${prefix}.pairs.stat \\ $input - echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //') + END_VERSIONS """ } diff --git a/modules/pairtools/dedup/meta.yml b/modules/pairtools/dedup/meta.yml index 888a52ff..d5a8ae87 100644 --- a/modules/pairtools/dedup/meta.yml +++ b/modules/pairtools/dedup/meta.yml @@ -30,7 +30,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - pairs: type: file description: Duplicates removed pairs diff --git a/modules/pairtools/flip/functions.nf b/modules/pairtools/flip/functions.nf index da9da093..85628ee0 100644 --- a/modules/pairtools/flip/functions.nf +++ b/modules/pairtools/flip/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pairtools/flip/main.nf b/modules/pairtools/flip/main.nf index efde6f55..3010b411 100644 --- a/modules/pairtools/flip/main.nf +++ b/modules/pairtools/flip/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process PAIRTOOLS_FLIP { output: tuple val(meta), path("*.flip.gz"), emit: flip - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process PAIRTOOLS_FLIP { -o ${prefix}.flip.gz \\ $sam - echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //') + END_VERSIONS """ } diff --git a/modules/pairtools/flip/meta.yml b/modules/pairtools/flip/meta.yml index 50badc23..981e3828 100644 --- a/modules/pairtools/flip/meta.yml +++ b/modules/pairtools/flip/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - flip: type: file description: output file of flip diff --git a/modules/pairtools/parse/functions.nf b/modules/pairtools/parse/functions.nf index da9da093..85628ee0 100644 --- a/modules/pairtools/parse/functions.nf +++ b/modules/pairtools/parse/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pairtools/parse/main.nf b/modules/pairtools/parse/main.nf index ad3169e1..66c9257b 100644 --- a/modules/pairtools/parse/main.nf +++ b/modules/pairtools/parse/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process PAIRTOOLS_PARSE { output: tuple val(meta), path("*.pairsam.gz") , emit: pairsam tuple val(meta), path("*.pairsam.stat"), emit: stat - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process PAIRTOOLS_PARSE { -o ${prefix}.pairsam.gz \\ $bam - echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //') + END_VERSIONS """ } diff --git a/modules/pairtools/parse/meta.yml b/modules/pairtools/parse/meta.yml index 311aa0ec..940fe5d1 100644 --- a/modules/pairtools/parse/meta.yml +++ b/modules/pairtools/parse/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - pairsam: type: file description: parsed pair file diff --git a/modules/pairtools/restrict/functions.nf b/modules/pairtools/restrict/functions.nf index da9da093..85628ee0 100644 --- a/modules/pairtools/restrict/functions.nf +++ b/modules/pairtools/restrict/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pairtools/restrict/main.nf b/modules/pairtools/restrict/main.nf index b9d7c7c7..31f463ad 100644 --- a/modules/pairtools/restrict/main.nf +++ b/modules/pairtools/restrict/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process PAIRTOOLS_RESTRICT { output: tuple val(meta), path("*.pairs.gz"), emit: restrict - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process PAIRTOOLS_RESTRICT { -o ${prefix}.pairs.gz \\ $pairs - echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //') + END_VERSIONS """ } diff --git a/modules/pairtools/restrict/meta.yml b/modules/pairtools/restrict/meta.yml index 28b8eabc..9dfb8f76 100644 --- a/modules/pairtools/restrict/meta.yml +++ b/modules/pairtools/restrict/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - restrict: type: file description: Filtered pairs file diff --git a/modules/pairtools/select/functions.nf b/modules/pairtools/select/functions.nf index da9da093..85628ee0 100644 --- a/modules/pairtools/select/functions.nf +++ b/modules/pairtools/select/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pairtools/select/main.nf b/modules/pairtools/select/main.nf index 680ad555..c9218ea9 100644 --- a/modules/pairtools/select/main.nf +++ b/modules/pairtools/select/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process PAIRTOOLS_SELECT { output: tuple val(meta), path("*.selected.pairs.gz") , emit: selected tuple val(meta), path("*.unselected.pairs.gz"), emit: unselected - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process PAIRTOOLS_SELECT { --output-rest ${prefix}.unselected.pairs.gz \\ ${input} - echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //') + END_VERSIONS """ } diff --git a/modules/pairtools/select/meta.yml b/modules/pairtools/select/meta.yml index cf256de2..18e97e99 100644 --- a/modules/pairtools/select/meta.yml +++ b/modules/pairtools/select/meta.yml @@ -30,7 +30,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - selected: type: file description: Selected pairs file diff --git a/modules/pairtools/sort/functions.nf b/modules/pairtools/sort/functions.nf index da9da093..85628ee0 100644 --- a/modules/pairtools/sort/functions.nf +++ b/modules/pairtools/sort/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pairtools/sort/main.nf b/modules/pairtools/sort/main.nf index d169d354..27caed7b 100644 --- a/modules/pairtools/sort/main.nf +++ b/modules/pairtools/sort/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process PAIRTOOLS_SORT { output: tuple val(meta), path("*.pairs.gz"), emit: sorted - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -38,6 +38,9 @@ process PAIRTOOLS_SORT { -o ${prefix}.pairs.gz \\ $input - echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //') + END_VERSIONS """ } diff --git a/modules/pairtools/sort/meta.yml b/modules/pairtools/sort/meta.yml index 565961bc..6f36323c 100644 --- a/modules/pairtools/sort/meta.yml +++ b/modules/pairtools/sort/meta.yml @@ -30,7 +30,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - sorted: type: file description: Sorted pairs file diff --git a/modules/pangolin/functions.nf b/modules/pangolin/functions.nf index da9da093..85628ee0 100644 --- a/modules/pangolin/functions.nf +++ b/modules/pangolin/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pangolin/main.nf b/modules/pangolin/main.nf index 5639dd00..5292d1c3 100644 --- a/modules/pangolin/main.nf +++ b/modules/pangolin/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process PANGOLIN { output: tuple val(meta), path('*.csv'), emit: report - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process PANGOLIN { --threads $task.cpus \\ $options.args - echo \$(pangolin --version) | sed "s/pangolin //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pangolin --version | sed "s/pangolin //g") + END_VERSIONS """ } diff --git a/modules/pangolin/meta.yml b/modules/pangolin/meta.yml index 2b2eb952..b1b583e9 100644 --- a/modules/pangolin/meta.yml +++ b/modules/pangolin/meta.yml @@ -27,7 +27,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/pbccs/functions.nf b/modules/pbccs/functions.nf index da9da093..85628ee0 100644 --- a/modules/pbccs/functions.nf +++ b/modules/pbccs/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pbccs/main.nf b/modules/pbccs/main.nf index 95f9908c..ccf17cc4 100644 --- a/modules/pbccs/main.nf +++ b/modules/pbccs/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -29,7 +29,7 @@ process PBCCS { tuple val(meta), path("*.ccs_report.txt" ) , emit: ccs_report_txt tuple val(meta), path("*.ccs_report.json" ) , emit: ccs_report_json tuple val(meta), path("*.zmw_metrics.json.gz"), emit: zmw_metrics - tuple val(meta), path("*.version.txt" ) , emit: version + tuple val(meta), path("versions.yml" ) , emit: version script: def software = getSoftwareName(task.process) @@ -49,6 +49,9 @@ process PBCCS { -j $task.cpus \\ $options.args - echo \$(ccs --version 2>&1) | grep -e 'commit' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(ccs --version 2>&1 | grep -e 'commit') + END_VERSIONS """ } diff --git a/modules/pbccs/meta.yml b/modules/pbccs/meta.yml index 8ed27abc..eb89d628 100644 --- a/modules/pbccs/meta.yml +++ b/modules/pbccs/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - css: type: file description: Consensus sequences diff --git a/modules/phantompeakqualtools/functions.nf b/modules/phantompeakqualtools/functions.nf index da9da093..85628ee0 100644 --- a/modules/phantompeakqualtools/functions.nf +++ b/modules/phantompeakqualtools/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/phantompeakqualtools/main.nf b/modules/phantompeakqualtools/main.nf index 7656420f..166ed8be 100644 --- a/modules/phantompeakqualtools/main.nf +++ b/modules/phantompeakqualtools/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process PHANTOMPEAKQUALTOOLS { tuple val(meta), path("*.out") , emit: spp tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.Rdata"), emit: rdata - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process PHANTOMPEAKQUALTOOLS { """ RUN_SPP=`which run_spp.R` Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/picard/collectmultiplemetrics/functions.nf b/modules/picard/collectmultiplemetrics/functions.nf index da9da093..85628ee0 100644 --- a/modules/picard/collectmultiplemetrics/functions.nf +++ b/modules/picard/collectmultiplemetrics/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf index 81547e84..11ddee9b 100644 --- a/modules/picard/collectmultiplemetrics/main.nf +++ b/modules/picard/collectmultiplemetrics/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { output: tuple val(meta), path("*_metrics"), emit: metrics tuple val(meta), path("*.pdf") , emit: pdf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -45,6 +45,9 @@ process PICARD_COLLECTMULTIPLEMETRICS { OUTPUT=${prefix}.CollectMultipleMetrics \\ REFERENCE_SEQUENCE=$fasta - echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version.*' | cut -f2- -d: > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) + END_VERSIONS """ } diff --git a/modules/picard/collectmultiplemetrics/meta.yml b/modules/picard/collectmultiplemetrics/meta.yml index 34006093..a588fd98 100644 --- a/modules/picard/collectmultiplemetrics/meta.yml +++ b/modules/picard/collectmultiplemetrics/meta.yml @@ -44,6 +44,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" diff --git a/modules/picard/collectwgsmetrics/functions.nf b/modules/picard/collectwgsmetrics/functions.nf index da9da093..85628ee0 100644 --- a/modules/picard/collectwgsmetrics/functions.nf +++ b/modules/picard/collectwgsmetrics/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf index 2f01354c..b5d11839 100644 --- a/modules/picard/collectwgsmetrics/main.nf +++ b/modules/picard/collectwgsmetrics/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process PICARD_COLLECTWGSMETRICS { output: tuple val(meta), path("*_metrics"), emit: metrics - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -44,6 +44,9 @@ process PICARD_COLLECTWGSMETRICS { OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\ REFERENCE_SEQUENCE=$fasta - echo \$(picard CollectWgsMetrics --version 2>&1) | grep -o 'Version.*' | cut -f2- -d: > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) + END_VERSIONS """ } diff --git a/modules/picard/collectwgsmetrics/meta.yml b/modules/picard/collectwgsmetrics/meta.yml index d8a2d9fb..ec828af5 100644 --- a/modules/picard/collectwgsmetrics/meta.yml +++ b/modules/picard/collectwgsmetrics/meta.yml @@ -39,7 +39,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@flowuenne" diff --git a/modules/picard/filtersamreads/functions.nf b/modules/picard/filtersamreads/functions.nf index da9da093..85628ee0 100644 --- a/modules/picard/filtersamreads/functions.nf +++ b/modules/picard/filtersamreads/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf index 22b8c5a8..c7e40d27 100644 --- a/modules/picard/filtersamreads/main.nf +++ b/modules/picard/filtersamreads/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process PICARD_FILTERSAMREADS { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -45,7 +45,10 @@ process PICARD_FILTERSAMREADS { --FILTER $filter \\ $options.args - echo \$(picard FilterSamReads --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(picard FilterSamReads --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS """ } else if ( filter == 'includeReadList' || filter == 'excludeReadList' ) { """ @@ -58,7 +61,10 @@ process PICARD_FILTERSAMREADS { --READ_LIST_FILE $readlist \\ $options.args - echo \$(picard FilterSamReads --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(picard FilterSamReads --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS """ } } diff --git a/modules/picard/filtersamreads/meta.yml b/modules/picard/filtersamreads/meta.yml index b5beba90..82f78065 100644 --- a/modules/picard/filtersamreads/meta.yml +++ b/modules/picard/filtersamreads/meta.yml @@ -45,7 +45,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@jfy133" diff --git a/modules/picard/markduplicates/functions.nf b/modules/picard/markduplicates/functions.nf index da9da093..85628ee0 100644 --- a/modules/picard/markduplicates/functions.nf +++ b/modules/picard/markduplicates/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf index ac829515..62cd10c2 100644 --- a/modules/picard/markduplicates/main.nf +++ b/modules/picard/markduplicates/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process PICARD_MARKDUPLICATES { tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.metrics.txt"), emit: metrics - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -45,6 +45,9 @@ process PICARD_MARKDUPLICATES { -O ${prefix}.bam \\ -M ${prefix}.MarkDuplicates.metrics.txt - echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(picard MarkDuplicates --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS """ } diff --git a/modules/picard/markduplicates/meta.yml b/modules/picard/markduplicates/meta.yml index b651b3a0..db72b5c5 100644 --- a/modules/picard/markduplicates/meta.yml +++ b/modules/picard/markduplicates/meta.yml @@ -45,7 +45,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@projectoriented" diff --git a/modules/picard/mergesamfiles/functions.nf b/modules/picard/mergesamfiles/functions.nf index da9da093..85628ee0 100644 --- a/modules/picard/mergesamfiles/functions.nf +++ b/modules/picard/mergesamfiles/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf index 9fd28af6..e9cba284 100644 --- a/modules/picard/mergesamfiles/main.nf +++ b/modules/picard/mergesamfiles/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process PICARD_MERGESAMFILES { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -43,12 +43,18 @@ process PICARD_MERGESAMFILES { $options.args \\ ${'INPUT='+bam_files.join(' INPUT=')} \\ OUTPUT=${prefix}.bam - echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(picard MergeSamFiles --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS """ } else { """ ln -s ${bam_files[0]} ${prefix}.bam - echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(picard MergeSamFiles --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS """ } } diff --git a/modules/picard/mergesamfiles/meta.yml b/modules/picard/mergesamfiles/meta.yml index 4ea9fd17..82ba2a43 100644 --- a/modules/picard/mergesamfiles/meta.yml +++ b/modules/picard/mergesamfiles/meta.yml @@ -35,6 +35,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" diff --git a/modules/picard/sortsam/functions.nf b/modules/picard/sortsam/functions.nf index da9da093..85628ee0 100644 --- a/modules/picard/sortsam/functions.nf +++ b/modules/picard/sortsam/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf index bb815c8f..475a30f9 100644 --- a/modules/picard/sortsam/main.nf +++ b/modules/picard/sortsam/main.nf @@ -1,6 +1,6 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process PICARD_SORTSAM { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -44,6 +44,9 @@ process PICARD_SORTSAM { --OUTPUT ${prefix}.bam \\ --SORT_ORDER $sort_order - echo \$(picard SortSam --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(picard SortSam --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS """ } diff --git a/modules/picard/sortsam/meta.yml b/modules/picard/sortsam/meta.yml index 42de6eab..37d12b91 100644 --- a/modules/picard/sortsam/meta.yml +++ b/modules/picard/sortsam/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: Sorted BAM/CRAM/SAM file diff --git a/modules/plasmidid/functions.nf b/modules/plasmidid/functions.nf index da9da093..85628ee0 100644 --- a/modules/plasmidid/functions.nf +++ b/modules/plasmidid/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/plasmidid/main.nf b/modules/plasmidid/main.nf index 986b6451..8be58c57 100644 --- a/modules/plasmidid/main.nf +++ b/modules/plasmidid/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -31,7 +31,7 @@ process PLASMIDID { tuple val(meta), path("${prefix}/database/") , emit: database tuple val(meta), path("${prefix}/fasta_files/") , emit: fasta_files tuple val(meta), path("${prefix}/kmer/") , emit: kmer - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -45,6 +45,9 @@ process PLASMIDID { -o . mv NO_GROUP/$prefix ./$prefix - echo \$(plasmidID --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(plasmidID --version 2>&1) + END_VERSIONS """ } diff --git a/modules/plasmidid/meta.yml b/modules/plasmidid/meta.yml index b7b188f8..a2689ddf 100644 --- a/modules/plasmidid/meta.yml +++ b/modules/plasmidid/meta.yml @@ -69,7 +69,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" diff --git a/modules/plink/vcf/functions.nf b/modules/plink/vcf/functions.nf index da9da093..85628ee0 100644 --- a/modules/plink/vcf/functions.nf +++ b/modules/plink/vcf/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/plink/vcf/main.nf b/modules/plink/vcf/main.nf index 39cc3825..697be55e 100644 --- a/modules/plink/vcf/main.nf +++ b/modules/plink/vcf/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process PLINK_VCF { tuple val(meta), path("*.bim"), emit: bim, optional: true tuple val(meta), path("*.fam"), emit: fam, optional: true - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process PLINK_VCF { --threads $task.cpus \\ --out ${prefix} - echo \$(plink --version 2>&1) | sed 's/^PLINK //' | sed 's/..-bit.*//'> ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + plink: \$( plink --version 2>&1 | sed 's/^PLINK //' | sed 's/..-bit.*//' ) + END_VERSIONS """ } diff --git a/modules/plink/vcf/meta.yml b/modules/plink/vcf/meta.yml index 8673158b..146a0030 100644 --- a/modules/plink/vcf/meta.yml +++ b/modules/plink/vcf/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bed: type: file description: PLINK binary biallelic genotype table diff --git a/modules/preseq/lcextrap/functions.nf b/modules/preseq/lcextrap/functions.nf index da9da093..85628ee0 100644 --- a/modules/preseq/lcextrap/functions.nf +++ b/modules/preseq/lcextrap/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/preseq/lcextrap/main.nf b/modules/preseq/lcextrap/main.nf index 2f601e4f..059b81f6 100644 --- a/modules/preseq/lcextrap/main.nf +++ b/modules/preseq/lcextrap/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process PRESEQ_LCEXTRAP { output: tuple val(meta), path("*.ccurve.txt"), emit: ccurve tuple val(meta), path("*.log") , emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -40,6 +40,9 @@ process PRESEQ_LCEXTRAP { $bam cp .command.err ${prefix}.command.log - echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(preseq 2>&1 | sed 's/^.*Version: //; s/Usage:.*\$//') + END_VERSIONS """ } diff --git a/modules/preseq/lcextrap/meta.yml b/modules/preseq/lcextrap/meta.yml index d1716231..616d8243 100755 --- a/modules/preseq/lcextrap/meta.yml +++ b/modules/preseq/lcextrap/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - ccurve: type: file description: File containing output of Preseq lcextrap diff --git a/modules/prodigal/functions.nf b/modules/prodigal/functions.nf index da9da093..85628ee0 100644 --- a/modules/prodigal/functions.nf +++ b/modules/prodigal/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/prodigal/main.nf b/modules/prodigal/main.nf index 5b73d6f1..6944f86b 100644 --- a/modules/prodigal/main.nf +++ b/modules/prodigal/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process PRODIGAL { tuple val(meta), path("${prefix}.fna"), emit: nucleotide_fasta tuple val(meta), path("${prefix}.faa"), emit: amino_acid_fasta tuple val(meta), path("${prefix}_all.txt"), emit: all_gene_annotations - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,6 +41,9 @@ process PRODIGAL { -a "${prefix}.faa" \\ -s "${prefix}_all.txt" - echo \$(prodigal -v 2>&1) | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p') + END_VERSIONS """ } diff --git a/modules/prodigal/meta.yml b/modules/prodigal/meta.yml index f48fe96d..c24ca4a3 100644 --- a/modules/prodigal/meta.yml +++ b/modules/prodigal/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: Sorted BAM/CRAM/SAM file diff --git a/modules/prokka/functions.nf b/modules/prokka/functions.nf index da9da093..85628ee0 100644 --- a/modules/prokka/functions.nf +++ b/modules/prokka/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/prokka/main.nf b/modules/prokka/main.nf index 1fa3f3d9..c2a9d682 100644 --- a/modules/prokka/main.nf +++ b/modules/prokka/main.nf @@ -1,4 +1,4 @@ -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -35,7 +35,7 @@ process PROKKA { tuple val(meta), path("${prefix}/*.log"), emit: log tuple val(meta), path("${prefix}/*.txt"), emit: txt tuple val(meta), path("${prefix}/*.tsv"), emit: tsv - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -51,6 +51,9 @@ process PROKKA { $prodigal_tf \\ $fasta - echo \$(prokka --version 2>&1) | sed 's/^.*prokka //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(prokka --version 2>&1 | sed 's/^.*prokka //') + END_VERSIONS """ } diff --git a/modules/prokka/meta.yml b/modules/prokka/meta.yml index 4489b2fd..26fb767a 100644 --- a/modules/prokka/meta.yml +++ b/modules/prokka/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - gff: type: file description: annotation in GFF3 format, containing both sequences and annotations diff --git a/modules/pycoqc/functions.nf b/modules/pycoqc/functions.nf index da9da093..85628ee0 100644 --- a/modules/pycoqc/functions.nf +++ b/modules/pycoqc/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pycoqc/main.nf b/modules/pycoqc/main.nf index 3f010247..f3b164ee 100644 --- a/modules/pycoqc/main.nf +++ b/modules/pycoqc/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process PYCOQC { output: path "*.html" , emit: html path "*.json" , emit: json - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process PYCOQC { -o pycoqc.html \\ -j pycoqc.json - echo \$(pycoQC --version 2>&1) | sed 's/^.*pycoQC v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pycoQC --version 2>&1 | sed 's/^.*pycoQC v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/pycoqc/meta.yml b/modules/pycoqc/meta.yml index 059b2f15..32012e83 100644 --- a/modules/pycoqc/meta.yml +++ b/modules/pycoqc/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" diff --git a/modules/pydamage/analyze/functions.nf b/modules/pydamage/analyze/functions.nf index da9da093..85628ee0 100644 --- a/modules/pydamage/analyze/functions.nf +++ b/modules/pydamage/analyze/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pydamage/analyze/main.nf b/modules/pydamage/analyze/main.nf index 5a2f331b..042e6c74 100644 --- a/modules/pydamage/analyze/main.nf +++ b/modules/pydamage/analyze/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process PYDAMAGE_ANALYZE { output: tuple val(meta), path("pydamage_results/pydamage_results.csv"), emit: csv - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process PYDAMAGE_ANALYZE { -p $task.cpus \\ $bam - echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pydamage --version 2>&1 | sed -e 's/pydamage, version //g') + END_VERSIONS """ } diff --git a/modules/pydamage/analyze/meta.yml b/modules/pydamage/analyze/meta.yml index 3da9f793..7369a3a3 100644 --- a/modules/pydamage/analyze/meta.yml +++ b/modules/pydamage/analyze/meta.yml @@ -45,7 +45,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - csv: type: file description: PyDamage results as csv files diff --git a/modules/pydamage/filter/functions.nf b/modules/pydamage/filter/functions.nf index da9da093..85628ee0 100644 --- a/modules/pydamage/filter/functions.nf +++ b/modules/pydamage/filter/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/pydamage/filter/main.nf b/modules/pydamage/filter/main.nf index 0010a7e0..9cb95b4a 100644 --- a/modules/pydamage/filter/main.nf +++ b/modules/pydamage/filter/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process PYDAMAGE_FILTER { output: tuple val(meta), path("pydamage_results/pydamage_filtered_results.csv"), emit: csv - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process PYDAMAGE_FILTER { $options.args \\ $csv - echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(pydamage --version 2>&1 | sed -e 's/pydamage, version //g') + END_VERSIONS """ } diff --git a/modules/pydamage/filter/meta.yml b/modules/pydamage/filter/meta.yml index 0870636b..29d4642b 100644 --- a/modules/pydamage/filter/meta.yml +++ b/modules/pydamage/filter/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - csv: type: file description: PyDamage filtered results as csv file diff --git a/modules/qcat/functions.nf b/modules/qcat/functions.nf index da9da093..85628ee0 100644 --- a/modules/qcat/functions.nf +++ b/modules/qcat/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/qcat/main.nf b/modules/qcat/main.nf index 8fc0814a..be239816 100644 --- a/modules/qcat/main.nf +++ b/modules/qcat/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process QCAT { output: tuple val(meta), path("fastq/*.fastq.gz"), emit: reads - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -47,6 +47,9 @@ process QCAT { ## Zip fastq files gzip fastq/* - echo \$(qcat --version 2>&1) | sed 's/^.*qcat //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(qcat --version 2>&1 | sed 's/^.*qcat //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/qcat/meta.yml b/modules/qcat/meta.yml index 3280f26e..5946eaa8 100644 --- a/modules/qcat/meta.yml +++ b/modules/qcat/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/qualimap/bamqc/functions.nf b/modules/qualimap/bamqc/functions.nf index da9da093..85628ee0 100644 --- a/modules/qualimap/bamqc/functions.nf +++ b/modules/qualimap/bamqc/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/qualimap/bamqc/main.nf b/modules/qualimap/bamqc/main.nf index 463cde4c..17779e27 100644 --- a/modules/qualimap/bamqc/main.nf +++ b/modules/qualimap/bamqc/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process QUALIMAP_BAMQC { output: tuple val(meta), path("${prefix}"), emit: results - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -56,6 +56,9 @@ process QUALIMAP_BAMQC { -outdir $prefix \\ -nt $task.cpus - echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(qualimap 2>&1 | sed 's/^.*QualiMap v.//; s/Built.*\$//') + END_VERSIONS """ } diff --git a/modules/qualimap/bamqc/meta.yml b/modules/qualimap/bamqc/meta.yml index 3c608f31..74c3ffdf 100644 --- a/modules/qualimap/bamqc/meta.yml +++ b/modules/qualimap/bamqc/meta.yml @@ -44,6 +44,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@phue" diff --git a/modules/qualimap/rnaseq/functions.nf b/modules/qualimap/rnaseq/functions.nf index da9da093..85628ee0 100644 --- a/modules/qualimap/rnaseq/functions.nf +++ b/modules/qualimap/rnaseq/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/qualimap/rnaseq/main.nf b/modules/qualimap/rnaseq/main.nf index 96fe2cd4..d1ed1021 100644 --- a/modules/qualimap/rnaseq/main.nf +++ b/modules/qualimap/rnaseq/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process QUALIMAP_RNASEQ { output: tuple val(meta), path("${prefix}"), emit: results - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -52,6 +52,9 @@ process QUALIMAP_RNASEQ { $paired_end \\ -outdir $prefix - echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(qualimap 2>&1 | sed 's/^.*QualiMap v.//; s/Built.*\$//') + END_VERSIONS """ } diff --git a/modules/quast/functions.nf b/modules/quast/functions.nf index da9da093..85628ee0 100644 --- a/modules/quast/functions.nf +++ b/modules/quast/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/quast/main.nf b/modules/quast/main.nf index 0b94c410..97ff93e2 100644 --- a/modules/quast/main.nf +++ b/modules/quast/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process QUAST { output: path "${prefix}" , emit: results path '*.tsv' , emit: tsv - path '*.version.txt', emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -43,6 +43,9 @@ process QUAST { $options.args \\ ${consensus.join(' ')} ln -s ${prefix}/report.tsv - echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/quast/meta.yml b/modules/quast/meta.yml index cc79486e..742dc8f0 100644 --- a/modules/quast/meta.yml +++ b/modules/quast/meta.yml @@ -39,7 +39,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" diff --git a/modules/rapidnj/functions.nf b/modules/rapidnj/functions.nf index da9da093..85628ee0 100644 --- a/modules/rapidnj/functions.nf +++ b/modules/rapidnj/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rapidnj/main.nf b/modules/rapidnj/main.nf index 78ed7693..a46fbfe8 100644 --- a/modules/rapidnj/main.nf +++ b/modules/rapidnj/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process RAPIDNJ { output: path "*.sth" , emit: stockholm_alignment path "*.tre" , emit: phylogeny - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -39,6 +39,9 @@ process RAPIDNJ { -x rapidnj_phylogeny.tre # Doesn't appear to be a way of getting the version number - echo 2.3.2 > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo 2.3.2) + END_VERSIONS """ } diff --git a/modules/rapidnj/meta.yml b/modules/rapidnj/meta.yml index cf2c61fc..7f7da9b9 100644 --- a/modules/rapidnj/meta.yml +++ b/modules/rapidnj/meta.yml @@ -23,7 +23,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - phylogeny: type: file description: A phylogeny in Newick format diff --git a/modules/rasusa/functions.nf b/modules/rasusa/functions.nf index da9da093..85628ee0 100644 --- a/modules/rasusa/functions.nf +++ b/modules/rasusa/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rasusa/main.nf b/modules/rasusa/main.nf index f895e1a2..88f3a208 100644 --- a/modules/rasusa/main.nf +++ b/modules/rasusa/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process RASUSA { output: tuple val(meta), path('*.fastq.gz'), emit: reads - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process RASUSA { --genome-size $genome_size \\ --input $reads \\ $output - echo \$(rasusa --version 2>&1) | sed -e "s/rasusa //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(rasusa --version 2>&1 | sed -e "s/rasusa //g") + END_VERSIONS """ } diff --git a/modules/rasusa/meta.yml b/modules/rasusa/meta.yml index 074ab2f0..61cdbe0c 100644 --- a/modules/rasusa/meta.yml +++ b/modules/rasusa/meta.yml @@ -38,7 +38,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - reads: type: file description: Reads with subsampled coverage diff --git a/modules/raxmlng/functions.nf b/modules/raxmlng/functions.nf index da9da093..85628ee0 100644 --- a/modules/raxmlng/functions.nf +++ b/modules/raxmlng/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/raxmlng/main.nf b/modules/raxmlng/main.nf index 9f8597b5..7094eaa7 100644 --- a/modules/raxmlng/main.nf +++ b/modules/raxmlng/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process RAXMLNG { output: path "*.raxml.bestTree", emit: phylogeny path "*.raxml.support" , optional:true, emit: phylogeny_bootstrapped - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process RAXMLNG { --threads $task.cpus \\ --prefix output - echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(raxml-ng --version 2>&1 | sed 's/^.*RAxML-NG v. //; s/released.*\$//') + END_VERSIONS """ } diff --git a/modules/raxmlng/meta.yml b/modules/raxmlng/meta.yml index 1df98148..d5f755c5 100644 --- a/modules/raxmlng/meta.yml +++ b/modules/raxmlng/meta.yml @@ -23,7 +23,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - phylogeny: type: file description: A phylogeny in Newick format diff --git a/modules/rsem/calculateexpression/functions.nf b/modules/rsem/calculateexpression/functions.nf index da9da093..85628ee0 100644 --- a/modules/rsem/calculateexpression/functions.nf +++ b/modules/rsem/calculateexpression/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rsem/calculateexpression/main.nf b/modules/rsem/calculateexpression/main.nf index 1f9ab854..33f34904 100644 --- a/modules/rsem/calculateexpression/main.nf +++ b/modules/rsem/calculateexpression/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process RSEM_CALCULATEEXPRESSION { tuple val(meta), path("*.isoforms.results"), emit: counts_transcript tuple val(meta), path("*.stat") , emit: stat tuple val(meta), path("*.log") , emit: logs - path "*.version.txt" , emit: version + path "versions.yml" , emit: version tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star tuple val(meta), path("${prefix}.genome.bam") , optional:true, emit: bam_genome @@ -56,6 +56,9 @@ process RSEM_CALCULATEEXPRESSION { \$INDEX \\ $prefix - rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g") + END_VERSIONS """ } diff --git a/modules/rsem/calculateexpression/meta.yml b/modules/rsem/calculateexpression/meta.yml index f8577085..079751d3 100644 --- a/modules/rsem/calculateexpression/meta.yml +++ b/modules/rsem/calculateexpression/meta.yml @@ -45,7 +45,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam_star: type: file description: BAM file generated by STAR (optional) diff --git a/modules/rsem/preparereference/functions.nf b/modules/rsem/preparereference/functions.nf index da9da093..85628ee0 100644 --- a/modules/rsem/preparereference/functions.nf +++ b/modules/rsem/preparereference/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rsem/preparereference/main.nf b/modules/rsem/preparereference/main.nf index a378eb6b..560b5a63 100644 --- a/modules/rsem/preparereference/main.nf +++ b/modules/rsem/preparereference/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process RSEM_PREPAREREFERENCE { output: path "rsem" , emit: index path "rsem/*transcripts.fa", emit: transcript_fasta - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -50,7 +50,10 @@ process RSEM_PREPAREREFERENCE { $fasta \\ rsem/genome - rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g") + END_VERSIONS """ } else { """ @@ -61,7 +64,10 @@ process RSEM_PREPAREREFERENCE { $fasta \\ rsem/genome - rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g") + END_VERSIONS """ } } diff --git a/modules/rsem/preparereference/meta.yml b/modules/rsem/preparereference/meta.yml index d7c02154..5ccca28a 100644 --- a/modules/rsem/preparereference/meta.yml +++ b/modules/rsem/preparereference/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/rseqc/bamstat/functions.nf b/modules/rseqc/bamstat/functions.nf index da9da093..85628ee0 100644 --- a/modules/rseqc/bamstat/functions.nf +++ b/modules/rseqc/bamstat/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rseqc/bamstat/main.nf b/modules/rseqc/bamstat/main.nf index 913c3f53..fa71dd11 100644 --- a/modules/rseqc/bamstat/main.nf +++ b/modules/rseqc/bamstat/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process RSEQC_BAMSTAT { output: tuple val(meta), path("*.bam_stat.txt"), emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process RSEQC_BAMSTAT { $options.args \\ > ${prefix}.bam_stat.txt - bam_stat.py --version | sed -e "s/bam_stat.py //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bam_stat.py --version | sed -e "s/bam_stat.py //g") + END_VERSIONS """ } diff --git a/modules/rseqc/bamstat/meta.yml b/modules/rseqc/bamstat/meta.yml index ff00d8c9..adb81c1c 100644 --- a/modules/rseqc/bamstat/meta.yml +++ b/modules/rseqc/bamstat/meta.yml @@ -30,7 +30,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/rseqc/inferexperiment/functions.nf b/modules/rseqc/inferexperiment/functions.nf index da9da093..85628ee0 100644 --- a/modules/rseqc/inferexperiment/functions.nf +++ b/modules/rseqc/inferexperiment/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rseqc/inferexperiment/main.nf b/modules/rseqc/inferexperiment/main.nf index a887e6e6..a9842c0d 100644 --- a/modules/rseqc/inferexperiment/main.nf +++ b/modules/rseqc/inferexperiment/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process RSEQC_INFEREXPERIMENT { output: tuple val(meta), path("*.infer_experiment.txt"), emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process RSEQC_INFEREXPERIMENT { $options.args \\ > ${prefix}.infer_experiment.txt - infer_experiment.py --version | sed -e "s/infer_experiment.py //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g") + END_VERSIONS """ } diff --git a/modules/rseqc/inferexperiment/meta.yml b/modules/rseqc/inferexperiment/meta.yml index 366c3e33..f89f90d1 100644 --- a/modules/rseqc/inferexperiment/meta.yml +++ b/modules/rseqc/inferexperiment/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/rseqc/innerdistance/functions.nf b/modules/rseqc/innerdistance/functions.nf index da9da093..85628ee0 100644 --- a/modules/rseqc/innerdistance/functions.nf +++ b/modules/rseqc/innerdistance/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rseqc/innerdistance/main.nf b/modules/rseqc/innerdistance/main.nf index e2e8f909..d98780f1 100644 --- a/modules/rseqc/innerdistance/main.nf +++ b/modules/rseqc/innerdistance/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -28,7 +28,7 @@ process RSEQC_INNERDISTANCE { tuple val(meta), path("*mean.txt") , optional:true, emit: mean tuple val(meta), path("*.pdf") , optional:true, emit: pdf tuple val(meta), path("*.r") , optional:true, emit: rscript - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -43,11 +43,17 @@ process RSEQC_INNERDISTANCE { > stdout.txt head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt - inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g") + END_VERSIONS """ } else { """ - inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g") + END_VERSIONS """ } } diff --git a/modules/rseqc/innerdistance/meta.yml b/modules/rseqc/innerdistance/meta.yml index ed72c51c..5b2b5e79 100644 --- a/modules/rseqc/innerdistance/meta.yml +++ b/modules/rseqc/innerdistance/meta.yml @@ -49,7 +49,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/rseqc/junctionannotation/functions.nf b/modules/rseqc/junctionannotation/functions.nf index da9da093..85628ee0 100644 --- a/modules/rseqc/junctionannotation/functions.nf +++ b/modules/rseqc/junctionannotation/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rseqc/junctionannotation/main.nf b/modules/rseqc/junctionannotation/main.nf index 30bdcd11..cfb12d69 100644 --- a/modules/rseqc/junctionannotation/main.nf +++ b/modules/rseqc/junctionannotation/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -30,7 +30,7 @@ process RSEQC_JUNCTIONANNOTATION { tuple val(meta), path("*.Interact.bed"), optional:true, emit: interact_bed tuple val(meta), path("*junction.pdf") , optional:true, emit: pdf tuple val(meta), path("*events.pdf") , optional:true, emit: events_pdf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -43,6 +43,9 @@ process RSEQC_JUNCTIONANNOTATION { $options.args \\ 2> ${prefix}.junction_annotation.log - junction_annotation.py --version | sed -e "s/junction_annotation.py //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(junction_annotation.py --version | sed -e "s/junction_annotation.py //g") + END_VERSIONS """ } diff --git a/modules/rseqc/junctionannotation/meta.yml b/modules/rseqc/junctionannotation/meta.yml index 64926ce0..d96e7756 100644 --- a/modules/rseqc/junctionannotation/meta.yml +++ b/modules/rseqc/junctionannotation/meta.yml @@ -55,7 +55,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/rseqc/junctionsaturation/functions.nf b/modules/rseqc/junctionsaturation/functions.nf index da9da093..85628ee0 100644 --- a/modules/rseqc/junctionsaturation/functions.nf +++ b/modules/rseqc/junctionsaturation/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rseqc/junctionsaturation/main.nf b/modules/rseqc/junctionsaturation/main.nf index 837006d0..a5aa5461 100644 --- a/modules/rseqc/junctionsaturation/main.nf +++ b/modules/rseqc/junctionsaturation/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process RSEQC_JUNCTIONSATURATION { output: tuple val(meta), path("*.pdf"), emit: pdf tuple val(meta), path("*.r") , emit: rscript - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process RSEQC_JUNCTIONSATURATION { -o $prefix \\ $options.args - junction_saturation.py --version | sed -e "s/junction_saturation.py //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(junction_saturation.py --version | sed -e "s/junction_saturation.py //g") + END_VERSIONS """ } diff --git a/modules/rseqc/junctionsaturation/meta.yml b/modules/rseqc/junctionsaturation/meta.yml index 38008577..aaf44cdc 100644 --- a/modules/rseqc/junctionsaturation/meta.yml +++ b/modules/rseqc/junctionsaturation/meta.yml @@ -38,7 +38,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/rseqc/readdistribution/functions.nf b/modules/rseqc/readdistribution/functions.nf index da9da093..85628ee0 100644 --- a/modules/rseqc/readdistribution/functions.nf +++ b/modules/rseqc/readdistribution/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rseqc/readdistribution/main.nf b/modules/rseqc/readdistribution/main.nf index 1b09908e..56086c89 100644 --- a/modules/rseqc/readdistribution/main.nf +++ b/modules/rseqc/readdistribution/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process RSEQC_READDISTRIBUTION { output: tuple val(meta), path("*.read_distribution.txt"), emit: txt - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process RSEQC_READDISTRIBUTION { -r $bed \\ > ${prefix}.read_distribution.txt - read_distribution.py --version | sed -e "s/read_distribution.py //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(read_distribution.py --version | sed -e "s/read_distribution.py //g") + END_VERSIONS """ } diff --git a/modules/rseqc/readdistribution/meta.yml b/modules/rseqc/readdistribution/meta.yml index ce2b0f5a..7ffab04f 100644 --- a/modules/rseqc/readdistribution/meta.yml +++ b/modules/rseqc/readdistribution/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/rseqc/readduplication/functions.nf b/modules/rseqc/readduplication/functions.nf index da9da093..85628ee0 100644 --- a/modules/rseqc/readduplication/functions.nf +++ b/modules/rseqc/readduplication/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/rseqc/readduplication/main.nf b/modules/rseqc/readduplication/main.nf index c86b05b6..ca7c2b13 100644 --- a/modules/rseqc/readduplication/main.nf +++ b/modules/rseqc/readduplication/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process RSEQC_READDUPLICATION { tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.r") , emit: rscript - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process RSEQC_READDUPLICATION { -o $prefix \\ $options.args - read_duplication.py --version | sed -e "s/read_duplication.py //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(read_duplication.py --version | sed -e "s/read_duplication.py //g") + END_VERSIONS """ } diff --git a/modules/rseqc/readduplication/meta.yml b/modules/rseqc/readduplication/meta.yml index c43ea688..efc48c0d 100644 --- a/modules/rseqc/readduplication/meta.yml +++ b/modules/rseqc/readduplication/meta.yml @@ -45,7 +45,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/salmon/index/functions.nf b/modules/salmon/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/salmon/index/functions.nf +++ b/modules/salmon/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/salmon/index/main.nf b/modules/salmon/index/main.nf index e72ff121..df4e2ed8 100644 --- a/modules/salmon/index/main.nf +++ b/modules/salmon/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process SALMON_INDEX { output: path "salmon" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -46,6 +46,9 @@ process SALMON_INDEX { -d decoys.txt \\ $options.args \\ -i salmon - salmon --version | sed -e "s/salmon //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(salmon --version | sed -e "s/salmon //g") + END_VERSIONS """ } diff --git a/modules/salmon/index/meta.yml b/modules/salmon/index/meta.yml index 652e2a77..4d16b359 100644 --- a/modules/salmon/index/meta.yml +++ b/modules/salmon/index/meta.yml @@ -28,7 +28,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/salmon/quant/functions.nf b/modules/salmon/quant/functions.nf index da9da093..85628ee0 100644 --- a/modules/salmon/quant/functions.nf +++ b/modules/salmon/quant/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/salmon/quant/main.nf b/modules/salmon/quant/main.nf index 1b9b5803..92d85f58 100644 --- a/modules/salmon/quant/main.nf +++ b/modules/salmon/quant/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -28,7 +28,7 @@ process SALMON_QUANT { output: tuple val(meta), path("${prefix}"), emit: results - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -72,6 +72,9 @@ process SALMON_QUANT { $options.args \\ -o $prefix - salmon --version | sed -e "s/salmon //g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(salmon --version | sed -e "s/salmon //g") + END_VERSIONS """ } diff --git a/modules/salmon/quant/meta.yml b/modules/salmon/quant/meta.yml index f37c9884..981df89e 100644 --- a/modules/salmon/quant/meta.yml +++ b/modules/salmon/quant/meta.yml @@ -48,7 +48,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/samtools/ampliconclip/functions.nf b/modules/samtools/ampliconclip/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/ampliconclip/functions.nf +++ b/modules/samtools/ampliconclip/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/ampliconclip/main.nf b/modules/samtools/ampliconclip/main.nf index 6ec27ccf..4a08026e 100644 --- a/modules/samtools/ampliconclip/main.nf +++ b/modules/samtools/ampliconclip/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -28,7 +28,7 @@ process SAMTOOLS_AMPLICONCLIP { tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.clipstats.txt") , optional:true, emit: stats tuple val(meta), path("*.cliprejects.bam"), optional:true, emit: rejects_bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -46,6 +46,9 @@ process SAMTOOLS_AMPLICONCLIP { -o ${prefix}.bam \\ $bam - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/ampliconclip/meta.yml b/modules/samtools/ampliconclip/meta.yml index fce06986..2ecbf463 100644 --- a/modules/samtools/ampliconclip/meta.yml +++ b/modules/samtools/ampliconclip/meta.yml @@ -46,7 +46,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: Clipped reads BAM file diff --git a/modules/samtools/faidx/functions.nf b/modules/samtools/faidx/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/faidx/functions.nf +++ b/modules/samtools/faidx/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf index a89ff2bb..fad14602 100644 --- a/modules/samtools/faidx/main.nf +++ b/modules/samtools/faidx/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,12 +23,15 @@ process SAMTOOLS_FAIDX { output: path "*.fai" , emit: fai - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ samtools faidx $fasta - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/faidx/meta.yml b/modules/samtools/faidx/meta.yml index f92234d0..77d21861 100644 --- a/modules/samtools/faidx/meta.yml +++ b/modules/samtools/faidx/meta.yml @@ -25,7 +25,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/samtools/fastq/functions.nf b/modules/samtools/fastq/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/fastq/functions.nf +++ b/modules/samtools/fastq/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/fastq/main.nf b/modules/samtools/fastq/main.nf index 6bedbb4e..73d32db8 100644 --- a/modules/samtools/fastq/main.nf +++ b/modules/samtools/fastq/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process SAMTOOLS_FASTQ { output: tuple val(meta), path("*.fastq.gz"), emit: fastq - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process SAMTOOLS_FASTQ { -@ $task.cpus \\ $endedness \\ $bam - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/fastq/meta.yml b/modules/samtools/fastq/meta.yml index ce269552..7c4cc488 100644 --- a/modules/samtools/fastq/meta.yml +++ b/modules/samtools/fastq/meta.yml @@ -37,6 +37,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@suzannejin" diff --git a/modules/samtools/flagstat/functions.nf b/modules/samtools/flagstat/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/flagstat/functions.nf +++ b/modules/samtools/flagstat/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf index d4852c66..70c04b23 100644 --- a/modules/samtools/flagstat/main.nf +++ b/modules/samtools/flagstat/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,12 +23,15 @@ process SAMTOOLS_FLAGSTAT { output: tuple val(meta), path("*.flagstat"), emit: flagstat - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ samtools flagstat $bam > ${bam}.flagstat - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/flagstat/meta.yml b/modules/samtools/flagstat/meta.yml index 8414bf54..d40e45b4 100644 --- a/modules/samtools/flagstat/meta.yml +++ b/modules/samtools/flagstat/meta.yml @@ -43,6 +43,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" diff --git a/modules/samtools/idxstats/functions.nf b/modules/samtools/idxstats/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/idxstats/functions.nf +++ b/modules/samtools/idxstats/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf index 14a07cfb..33605f30 100644 --- a/modules/samtools/idxstats/main.nf +++ b/modules/samtools/idxstats/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,12 +23,15 @@ process SAMTOOLS_IDXSTATS { output: tuple val(meta), path("*.idxstats"), emit: idxstats - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ samtools idxstats $bam > ${bam}.idxstats - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/idxstats/meta.yml b/modules/samtools/idxstats/meta.yml index 530d0772..93e8f694 100644 --- a/modules/samtools/idxstats/meta.yml +++ b/modules/samtools/idxstats/meta.yml @@ -44,6 +44,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" diff --git a/modules/samtools/index/functions.nf b/modules/samtools/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/index/functions.nf +++ b/modules/samtools/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf index e1966fb3..83802d95 100644 --- a/modules/samtools/index/main.nf +++ b/modules/samtools/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,12 +24,15 @@ process SAMTOOLS_INDEX { output: tuple val(meta), path("*.bai"), optional:true, emit: bai tuple val(meta), path("*.csi"), optional:true, emit: csi - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ samtools index $options.args $bam - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/index/meta.yml b/modules/samtools/index/meta.yml index 5d076e3b..6f7dc887 100644 --- a/modules/samtools/index/meta.yml +++ b/modules/samtools/index/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/samtools/merge/functions.nf b/modules/samtools/merge/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/merge/functions.nf +++ b/modules/samtools/merge/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf index 0182b9fd..85a41926 100644 --- a/modules/samtools/merge/main.nf +++ b/modules/samtools/merge/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process SAMTOOLS_MERGE { output: tuple val(meta), path("${prefix}.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ samtools merge ${prefix}.bam $bams - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/merge/meta.yml b/modules/samtools/merge/meta.yml index 9092f22e..c5f15a14 100644 --- a/modules/samtools/merge/meta.yml +++ b/modules/samtools/merge/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@yuukiiwa " diff --git a/modules/samtools/mpileup/functions.nf b/modules/samtools/mpileup/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/mpileup/functions.nf +++ b/modules/samtools/mpileup/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf index f736e9c7..28185934 100644 --- a/modules/samtools/mpileup/main.nf +++ b/modules/samtools/mpileup/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process SAMTOOLS_MPILEUP { output: tuple val(meta), path("*.mpileup"), emit: mpileup - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process SAMTOOLS_MPILEUP { --output ${prefix}.mpileup \\ $options.args \\ $bam - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/mpileup/meta.yml b/modules/samtools/mpileup/meta.yml index 7e432a78..aa0ccc6d 100644 --- a/modules/samtools/mpileup/meta.yml +++ b/modules/samtools/mpileup/meta.yml @@ -41,7 +41,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/samtools/sort/functions.nf b/modules/samtools/sort/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/sort/functions.nf +++ b/modules/samtools/sort/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf index 0a6b7048..4c3c4c1f 100644 --- a/modules/samtools/sort/main.nf +++ b/modules/samtools/sort/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process SAMTOOLS_SORT { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ samtools sort $options.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/sort/meta.yml b/modules/samtools/sort/meta.yml index 704e8c1f..d4f70a8e 100644 --- a/modules/samtools/sort/meta.yml +++ b/modules/samtools/sort/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/samtools/stats/functions.nf b/modules/samtools/stats/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/stats/functions.nf +++ b/modules/samtools/stats/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf index 8c72d725..b1fd325f 100644 --- a/modules/samtools/stats/main.nf +++ b/modules/samtools/stats/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,12 +23,15 @@ process SAMTOOLS_STATS { output: tuple val(meta), path("*.stats"), emit: stats - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ samtools stats $bam > ${bam}.stats - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/stats/meta.yml b/modules/samtools/stats/meta.yml index b549ff5c..1c7dcc8b 100644 --- a/modules/samtools/stats/meta.yml +++ b/modules/samtools/stats/meta.yml @@ -42,6 +42,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" diff --git a/modules/samtools/view/functions.nf b/modules/samtools/view/functions.nf index da9da093..85628ee0 100644 --- a/modules/samtools/view/functions.nf +++ b/modules/samtools/view/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf index 2ca57032..824b9bab 100644 --- a/modules/samtools/view/main.nf +++ b/modules/samtools/view/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process SAMTOOLS_VIEW { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ samtools view $options.args $bam > ${prefix}.bam - echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/samtools/view/meta.yml b/modules/samtools/view/meta.yml index c35a8b03..6388f9bc 100644 --- a/modules/samtools/view/meta.yml +++ b/modules/samtools/view/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/seacr/callpeak/functions.nf b/modules/seacr/callpeak/functions.nf index da9da093..85628ee0 100644 --- a/modules/seacr/callpeak/functions.nf +++ b/modules/seacr/callpeak/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/seacr/callpeak/main.nf b/modules/seacr/callpeak/main.nf index 429c45cf..cc567dfb 100644 --- a/modules/seacr/callpeak/main.nf +++ b/modules/seacr/callpeak/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process SEACR_CALLPEAK { output: tuple val(meta), path("*.bed"), emit: bed - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process SEACR_CALLPEAK { $options.args \\ $prefix - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/seacr/callpeak/meta.yml b/modules/seacr/callpeak/meta.yml index 579961e2..80da69e4 100644 --- a/modules/seacr/callpeak/meta.yml +++ b/modules/seacr/callpeak/meta.yml @@ -43,6 +43,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@chris-cheshire" diff --git a/modules/seqkit/split2/functions.nf b/modules/seqkit/split2/functions.nf index da9da093..85628ee0 100644 --- a/modules/seqkit/split2/functions.nf +++ b/modules/seqkit/split2/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/seqkit/split2/main.nf b/modules/seqkit/split2/main.nf index 5eeb0ad0..44e0046f 100644 --- a/modules/seqkit/split2/main.nf +++ b/modules/seqkit/split2/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process SEQKIT_SPLIT2 { output: tuple val(meta), path("*.split/*.gz"), emit: reads - path("*.version.txt") , emit: version + path("versions.yml") , emit: version script: @@ -41,7 +41,10 @@ process SEQKIT_SPLIT2 { -1 ${reads} \ --out-dir ${prefix}.split - echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(seqkit --version 2>&1 | sed 's/^.*seqkit //; s/Using.*\$//') + END_VERSIONS """ } else { """ @@ -53,7 +56,10 @@ process SEQKIT_SPLIT2 { -2 ${reads[1]} \ --out-dir ${prefix}.split - echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(seqkit --version 2>&1 | sed 's/^.*seqkit //; s/Using.*\$//') + END_VERSIONS """ } } diff --git a/modules/seqkit/split2/meta.yml b/modules/seqkit/split2/meta.yml index 44ae4ea7..5dfee7f9 100644 --- a/modules/seqkit/split2/meta.yml +++ b/modules/seqkit/split2/meta.yml @@ -33,6 +33,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@FriederikeHanssen" diff --git a/modules/seqtk/sample/functions.nf b/modules/seqtk/sample/functions.nf index da9da093..85628ee0 100644 --- a/modules/seqtk/sample/functions.nf +++ b/modules/seqtk/sample/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/seqtk/sample/main.nf b/modules/seqtk/sample/main.nf index b50a5a2a..d62d8cac 100644 --- a/modules/seqtk/sample/main.nf +++ b/modules/seqtk/sample/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process SEQTK_SAMPLE { output: tuple val(meta), path("*.fastq.gz"), emit: reads - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -38,7 +38,10 @@ process SEQTK_SAMPLE { $sample_size \\ | gzip --no-name > ${prefix}.fastq.gz \\ - echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(seqtk 2>&1 | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS """ } else { if (!(options.args ==~ /.*-s[0-9]+.*/)) { @@ -59,7 +62,10 @@ process SEQTK_SAMPLE { $sample_size \\ | gzip --no-name > ${prefix}_2.fastq.gz \\ - echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(seqtk 2>&1 | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS """ } } diff --git a/modules/seqtk/sample/meta.yml b/modules/seqtk/sample/meta.yml index f9122936..b9422433 100644 --- a/modules/seqtk/sample/meta.yml +++ b/modules/seqtk/sample/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - reads: type: file description: Subsampled FastQ files, 1 for single-end data or 2 for paired-end data. diff --git a/modules/seqtk/subseq/functions.nf b/modules/seqtk/subseq/functions.nf index da9da093..85628ee0 100644 --- a/modules/seqtk/subseq/functions.nf +++ b/modules/seqtk/subseq/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/seqtk/subseq/main.nf b/modules/seqtk/subseq/main.nf index 810a8a48..2907d282 100644 --- a/modules/seqtk/subseq/main.nf +++ b/modules/seqtk/subseq/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process SEQTK_SUBSEQ { output: path "*.gz" , emit: sequences - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -41,6 +41,9 @@ process SEQTK_SUBSEQ { $filter_list | \\ gzip --no-name > ${sequences}${prefix}.${ext}.gz - echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(seqtk 2>&1 | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/seqtk/subseq/meta.yml b/modules/seqtk/subseq/meta.yml index 0676229d..f7c6c624 100644 --- a/modules/seqtk/subseq/meta.yml +++ b/modules/seqtk/subseq/meta.yml @@ -24,7 +24,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - sequences: type: file description: FASTQ/FASTA file diff --git a/modules/sequenzautils/bam2seqz/functions.nf b/modules/sequenzautils/bam2seqz/functions.nf index da9da093..85628ee0 100755 --- a/modules/sequenzautils/bam2seqz/functions.nf +++ b/modules/sequenzautils/bam2seqz/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/sequenzautils/bam2seqz/main.nf b/modules/sequenzautils/bam2seqz/main.nf index aec19725..ad4f6847 100644 --- a/modules/sequenzautils/bam2seqz/main.nf +++ b/modules/sequenzautils/bam2seqz/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process SEQUENZAUTILS_BAM2SEQZ { output: tuple val(meta), path("*.seqz.gz"), emit: seqz - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -40,6 +40,9 @@ process SEQUENZAUTILS_BAM2SEQZ { -gc $wigfile \\ -o ${prefix}.seqz.gz - echo \$(sequenzautils --version 2>&1) | sed 's/^.*sequenzautils //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(sequenzautils --version 2>&1 | sed 's/^.*sequenzautils //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/sequenzautils/bam2seqz/meta.yml b/modules/sequenzautils/bam2seqz/meta.yml index 171e155c..2ce4ab7f 100755 --- a/modules/sequenzautils/bam2seqz/meta.yml +++ b/modules/sequenzautils/bam2seqz/meta.yml @@ -40,7 +40,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - seqz: type: file description: Seqz file diff --git a/modules/sequenzautils/gcwiggle/functions.nf b/modules/sequenzautils/gcwiggle/functions.nf index da9da093..85628ee0 100755 --- a/modules/sequenzautils/gcwiggle/functions.nf +++ b/modules/sequenzautils/gcwiggle/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/sequenzautils/gcwiggle/main.nf b/modules/sequenzautils/gcwiggle/main.nf index fd200b6b..a0575d7e 100644 --- a/modules/sequenzautils/gcwiggle/main.nf +++ b/modules/sequenzautils/gcwiggle/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process SEQUENZAUTILS_GCWIGGLE { output: tuple val(meta), path("*.wig.gz"), emit: wig - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -35,6 +35,9 @@ process SEQUENZAUTILS_GCWIGGLE { --fasta $fasta \\ -o ${prefix}.wig.gz - echo \$(sequenzautils --version 2>&1) | sed 's/^.*sequenzautils //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(sequenzautils --version 2>&1 | sed 's/^.*sequenzautils //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/sequenzautils/gcwiggle/meta.yml b/modules/sequenzautils/gcwiggle/meta.yml index e1cb7b03..35daa498 100644 --- a/modules/sequenzautils/gcwiggle/meta.yml +++ b/modules/sequenzautils/gcwiggle/meta.yml @@ -28,7 +28,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - wig: type: file description: GC Wiggle track file diff --git a/modules/seqwish/induce/functions.nf b/modules/seqwish/induce/functions.nf index da9da093..85628ee0 100644 --- a/modules/seqwish/induce/functions.nf +++ b/modules/seqwish/induce/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/seqwish/induce/main.nf b/modules/seqwish/induce/main.nf index ebf714ff..e9b2836b 100644 --- a/modules/seqwish/induce/main.nf +++ b/modules/seqwish/induce/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process SEQWISH_INDUCE { output: tuple val(meta), path("*.gfa"), emit: gfa - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: @@ -39,6 +39,9 @@ process SEQWISH_INDUCE { --gfa=${prefix}.gfa \\ $options.args - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/seqwish/induce/meta.yml b/modules/seqwish/induce/meta.yml index f357f0df..c2836824 100644 --- a/modules/seqwish/induce/meta.yml +++ b/modules/seqwish/induce/meta.yml @@ -41,6 +41,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@heuermh" diff --git a/modules/shovill/functions.nf b/modules/shovill/functions.nf index da9da093..85628ee0 100644 --- a/modules/shovill/functions.nf +++ b/modules/shovill/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/shovill/main.nf b/modules/shovill/main.nf index e751b2a8..8319e75f 100644 --- a/modules/shovill/main.nf +++ b/modules/shovill/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process SHOVILL { tuple val(meta), path("shovill.log") , emit: log tuple val(meta), path("{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs tuple val(meta), path("contigs.{fastg,gfa,LastGraph}") , optional:true, emit: gfa - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process SHOVILL { --outdir ./ \\ --force - echo \$(shovill --version 2>&1) | sed 's/^.*shovill //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(shovill --version 2>&1 | sed 's/^.*shovill //' ) + END_VERSIONS """ } diff --git a/modules/shovill/meta.yml b/modules/shovill/meta.yml index b8f24e34..b878f93d 100644 --- a/modules/shovill/meta.yml +++ b/modules/shovill/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - contigs: type: file description: The final assembly produced by Shovill diff --git a/modules/snpdists/functions.nf b/modules/snpdists/functions.nf index da9da093..85628ee0 100644 --- a/modules/snpdists/functions.nf +++ b/modules/snpdists/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/snpdists/main.nf b/modules/snpdists/main.nf index c103bb33..ede94906 100644 --- a/modules/snpdists/main.nf +++ b/modules/snpdists/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process SNPDISTS { output: tuple val(meta), path("*.tsv"), emit: tsv - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process SNPDISTS { $options.args \\ $alignment > ${prefix}.tsv - echo \$(snp-dists -v 2>&1) | sed 's/snp-dists //;' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(snp-dists -v 2>&1 | sed 's/snp-dists //;') + END_VERSIONS """ } diff --git a/modules/snpdists/meta.yml b/modules/snpdists/meta.yml index 590d034a..e86e3092 100644 --- a/modules/snpdists/meta.yml +++ b/modules/snpdists/meta.yml @@ -36,6 +36,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@abhi18av" diff --git a/modules/snpeff/functions.nf b/modules/snpeff/functions.nf index da9da093..85628ee0 100644 --- a/modules/snpeff/functions.nf +++ b/modules/snpeff/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/snpeff/main.nf b/modules/snpeff/main.nf index af0fd816..aa25a092 100644 --- a/modules/snpeff/main.nf +++ b/modules/snpeff/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -31,7 +31,7 @@ process SNPEFF { output: tuple val(meta), path("*.ann.vcf"), emit: vcf path "*.csv" , emit: report - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -52,6 +52,9 @@ process SNPEFF { $vcf \\ > ${prefix}.ann.vcf - echo \$(snpEff -version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(snpEff -version 2>&1) + END_VERSIONS """ } diff --git a/modules/snpeff/meta.yml b/modules/snpeff/meta.yml index 7ba62cde..aa21e2bc 100644 --- a/modules/snpeff/meta.yml +++ b/modules/snpeff/meta.yml @@ -52,6 +52,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@maxulysse" diff --git a/modules/snpsites/functions.nf b/modules/snpsites/functions.nf index da9da093..85628ee0 100644 --- a/modules/snpsites/functions.nf +++ b/modules/snpsites/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/snpsites/main.nf b/modules/snpsites/main.nf index 5104572e..5cc85773 100644 --- a/modules/snpsites/main.nf +++ b/modules/snpsites/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process SNPSITES { output: path "*.fas" , emit: fasta path "*.sites.txt" , emit: constant_sites - path "*.version.txt", emit: version + path "versions.yml" , emit: version env CONSTANT_SITES, emit: constant_sites_string script: @@ -38,6 +38,9 @@ process SNPSITES { CONSTANT_SITES=\$(cat constant.sites.txt) - echo \$(snp-sites -V 2>&1) | sed 's/snp-sites //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(snp-sites -V 2>&1 | sed 's/snp-sites //') + END_VERSIONS """ } diff --git a/modules/snpsites/meta.yml b/modules/snpsites/meta.yml index 0a22b879..ae250e5f 100644 --- a/modules/snpsites/meta.yml +++ b/modules/snpsites/meta.yml @@ -18,7 +18,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - fasta: type: file description: Variant fasta file diff --git a/modules/sortmerna/functions.nf b/modules/sortmerna/functions.nf index da9da093..85628ee0 100644 --- a/modules/sortmerna/functions.nf +++ b/modules/sortmerna/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/sortmerna/main.nf b/modules/sortmerna/main.nf index 32ca4ca9..01975979 100644 --- a/modules/sortmerna/main.nf +++ b/modules/sortmerna/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process SORTMERNA { output: tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), path("*.log") , emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -47,7 +47,10 @@ process SORTMERNA { gzip -f < non_rRNA_reads.fq > ${prefix}.fastq.gz mv rRNA_reads.log ${prefix}.sortmerna.log - echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(sortmerna --version 2>&1 | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//') + END_VERSIONS """ } else { """ @@ -67,7 +70,10 @@ process SORTMERNA { gzip -f < non_rRNA_reads_rev.fq > ${prefix}_2.fastq.gz mv rRNA_reads.log ${prefix}.sortmerna.log - echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(sortmerna --version 2>&1 | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//') + END_VERSIONS """ } } diff --git a/modules/spades/functions.nf b/modules/spades/functions.nf index da9da093..85628ee0 100644 --- a/modules/spades/functions.nf +++ b/modules/spades/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/spades/main.nf b/modules/spades/main.nf index e78500f2..a260de54 100644 --- a/modules/spades/main.nf +++ b/modules/spades/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -29,7 +29,7 @@ process SPADES { tuple val(meta), path('*.gene_clusters.fa'), optional:true, emit: gene_clusters tuple val(meta), path('*.assembly.gfa') , optional:true, emit: gfa tuple val(meta), path('*.log') , emit: log - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -62,6 +62,9 @@ process SPADES { mv gene_clusters.fasta ${prefix}.gene_clusters.fa fi - echo \$(spades.py --version 2>&1) | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/spades/meta.yml b/modules/spades/meta.yml index 5a05e5f3..38c5c2ae 100644 --- a/modules/spades/meta.yml +++ b/modules/spades/meta.yml @@ -62,7 +62,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@JoseEspinosa" diff --git a/modules/staphopiasccmec/functions.nf b/modules/staphopiasccmec/functions.nf index da9da093..85628ee0 100644 --- a/modules/staphopiasccmec/functions.nf +++ b/modules/staphopiasccmec/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/staphopiasccmec/main.nf b/modules/staphopiasccmec/main.nf index 85a61514..0e57128b 100644 --- a/modules/staphopiasccmec/main.nf +++ b/modules/staphopiasccmec/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process STAPHOPIASCCMEC { output: tuple val(meta), path("*.tsv"), emit: tsv - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -31,6 +31,9 @@ process STAPHOPIASCCMEC { """ staphopia-sccmec --assembly $fasta $options.args > ${prefix}.tsv - echo \$(staphopia-sccmec --version 2>&1) | sed 's/^.*staphopia-sccmec //' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(staphopia-sccmec --version 2>&1 | sed 's/^.*staphopia-sccmec //') + END_VERSIONS """ } diff --git a/modules/staphopiasccmec/meta.yml b/modules/staphopiasccmec/meta.yml index 2054c6b3..e1ce3a05 100644 --- a/modules/staphopiasccmec/meta.yml +++ b/modules/staphopiasccmec/meta.yml @@ -34,7 +34,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - tsv: type: file description: Tab-delimited results diff --git a/modules/star/align/functions.nf b/modules/star/align/functions.nf index da9da093..85628ee0 100644 --- a/modules/star/align/functions.nf +++ b/modules/star/align/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/star/align/main.nf b/modules/star/align/main.nf index d5d88ce8..677d1f2a 100644 --- a/modules/star/align/main.nf +++ b/modules/star/align/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -29,7 +29,7 @@ process STAR_ALIGN { tuple val(meta), path('*Log.final.out') , emit: log_final tuple val(meta), path('*Log.out') , emit: log_out tuple val(meta), path('*Log.progress.out'), emit: log_progress - path '*.version.txt' , emit: version + path "versions.yml" , emit: version tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript @@ -68,6 +68,9 @@ process STAR_ALIGN { gzip ${prefix}.unmapped_2.fastq fi - STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g") + END_VERSIONS """ } diff --git a/modules/star/align/meta.yml b/modules/star/align/meta.yml index a589d145..7f0217ea 100644 --- a/modules/star/align/meta.yml +++ b/modules/star/align/meta.yml @@ -48,7 +48,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam_sorted: type: file description: Sorted BAM file of read alignments (optional) diff --git a/modules/star/genomegenerate/functions.nf b/modules/star/genomegenerate/functions.nf index da9da093..85628ee0 100644 --- a/modules/star/genomegenerate/functions.nf +++ b/modules/star/genomegenerate/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/star/genomegenerate/main.nf b/modules/star/genomegenerate/main.nf index 9335b9b5..5ccb38e8 100644 --- a/modules/star/genomegenerate/main.nf +++ b/modules/star/genomegenerate/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process STAR_GENOMEGENERATE { output: path "star" , emit: index - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -43,7 +43,10 @@ process STAR_GENOMEGENERATE { $memory \\ $options.args - STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g") + END_VERSIONS """ } else { """ @@ -61,7 +64,10 @@ process STAR_GENOMEGENERATE { $memory \\ $options.args - STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g") + END_VERSIONS """ } } diff --git a/modules/star/genomegenerate/meta.yml b/modules/star/genomegenerate/meta.yml index aae0219b..70525738 100644 --- a/modules/star/genomegenerate/meta.yml +++ b/modules/star/genomegenerate/meta.yml @@ -29,7 +29,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@kevinmenden" diff --git a/modules/strelka/germline/functions.nf b/modules/strelka/germline/functions.nf index da9da093..85628ee0 100644 --- a/modules/strelka/germline/functions.nf +++ b/modules/strelka/germline/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/strelka/germline/main.nf b/modules/strelka/germline/main.nf index 48f795b0..d2203fa4 100644 --- a/modules/strelka/germline/main.nf +++ b/modules/strelka/germline/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -29,7 +29,7 @@ process STRELKA_GERMLINE { tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi tuple val(meta), path("*genome.vcf.gz") , emit: genome_vcf tuple val(meta), path("*genome.vcf.gz.tbi") , emit: genome_vcf_tbi - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -49,6 +49,9 @@ process STRELKA_GERMLINE { mv strelka/results/variants/variants.vcf.gz ${prefix}.variants.vcf.gz mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}.variants.vcf.gz.tbi - echo configureStrelkaGermlineWorkflow.py --version &> ${software}.version.txt #2>&1 + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + strelka: \$( configureStrelkaGermlineWorkflow.py --version ) + END_VERSIONS """ } diff --git a/modules/strelka/germline/meta.yml b/modules/strelka/germline/meta.yml index ae0ecb47..4423e437 100644 --- a/modules/strelka/germline/meta.yml +++ b/modules/strelka/germline/meta.yml @@ -58,6 +58,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@arontommi" diff --git a/modules/stringtie/merge/functions.nf b/modules/stringtie/merge/functions.nf index da9da093..85628ee0 100644 --- a/modules/stringtie/merge/functions.nf +++ b/modules/stringtie/merge/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/stringtie/merge/main.nf b/modules/stringtie/merge/main.nf index f0820be1..85670a91 100644 --- a/modules/stringtie/merge/main.nf +++ b/modules/stringtie/merge/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process STRINGTIE_MERGE { output: path "stringtie.merged.gtf", emit: gtf - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process STRINGTIE_MERGE { -G $annotation_gtf \\ -o stringtie.merged.gtf - echo \$(stringtie --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(stringtie --version 2>&1) + END_VERSIONS """ } diff --git a/modules/stringtie/stringtie/functions.nf b/modules/stringtie/stringtie/functions.nf index da9da093..85628ee0 100644 --- a/modules/stringtie/stringtie/functions.nf +++ b/modules/stringtie/stringtie/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/stringtie/stringtie/main.nf b/modules/stringtie/stringtie/main.nf index 6cff993a..92986dba 100644 --- a/modules/stringtie/stringtie/main.nf +++ b/modules/stringtie/stringtie/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process STRINGTIE { tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf tuple val(meta), path("*.abundance.txt") , emit: abundance tuple val(meta), path("*.ballgown") , emit: ballgown - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -51,6 +51,9 @@ process STRINGTIE { -p $task.cpus \\ $options.args - echo \$(stringtie --version 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(stringtie --version 2>&1) + END_VERSIONS """ } diff --git a/modules/stringtie/stringtie/meta.yml b/modules/stringtie/stringtie/meta.yml index 52ec899d..f9363009 100644 --- a/modules/stringtie/stringtie/meta.yml +++ b/modules/stringtie/stringtie/meta.yml @@ -51,6 +51,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" diff --git a/modules/subread/featurecounts/functions.nf b/modules/subread/featurecounts/functions.nf index da9da093..85628ee0 100644 --- a/modules/subread/featurecounts/functions.nf +++ b/modules/subread/featurecounts/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/subread/featurecounts/main.nf b/modules/subread/featurecounts/main.nf index cde14a74..3e2eb765 100644 --- a/modules/subread/featurecounts/main.nf +++ b/modules/subread/featurecounts/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process SUBREAD_FEATURECOUNTS { output: tuple val(meta), path("*featureCounts.txt") , emit: counts tuple val(meta), path("*featureCounts.txt.summary"), emit: summary - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -47,6 +47,9 @@ process SUBREAD_FEATURECOUNTS { -o ${prefix}.featureCounts.txt \\ ${bams.join(' ')} - echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g" > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(featureCounts -v 2>&1 | sed -e "s/featureCounts v//g") + END_VERSIONS """ } diff --git a/modules/subread/featurecounts/meta.yml b/modules/subread/featurecounts/meta.yml index d24f70bd..504d2f48 100644 --- a/modules/subread/featurecounts/meta.yml +++ b/modules/subread/featurecounts/meta.yml @@ -46,7 +46,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@ntoda03" diff --git a/modules/tabix/bgzip/functions.nf b/modules/tabix/bgzip/functions.nf index da9da093..85628ee0 100644 --- a/modules/tabix/bgzip/functions.nf +++ b/modules/tabix/bgzip/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/tabix/bgzip/main.nf b/modules/tabix/bgzip/main.nf index e9d2e96e..eb95de62 100644 --- a/modules/tabix/bgzip/main.nf +++ b/modules/tabix/bgzip/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process TABIX_BGZIP { output: tuple val(meta), path("*.gz"), emit: gz - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -31,6 +31,9 @@ process TABIX_BGZIP { """ bgzip -c $options.args $input > ${prefix}.${input.getExtension()}.gz - echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//') + END_VERSIONS """ } diff --git a/modules/tabix/bgzip/meta.yml b/modules/tabix/bgzip/meta.yml index 686d72e6..801d98bc 100644 --- a/modules/tabix/bgzip/meta.yml +++ b/modules/tabix/bgzip/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/tabix/bgziptabix/functions.nf b/modules/tabix/bgziptabix/functions.nf index da9da093..85628ee0 100644 --- a/modules/tabix/bgziptabix/functions.nf +++ b/modules/tabix/bgziptabix/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf index 6cc3322f..7179a97e 100644 --- a/modules/tabix/bgziptabix/main.nf +++ b/modules/tabix/bgziptabix/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process TABIX_BGZIPTABIX { output: tuple val(meta), path("*.gz"), path("*.tbi"), emit: tbi - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -32,6 +32,9 @@ process TABIX_BGZIPTABIX { bgzip -c $options.args $input > ${prefix}.gz tabix $options.args2 ${prefix}.gz - echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//') + END_VERSIONS """ } diff --git a/modules/tabix/bgziptabix/meta.yml b/modules/tabix/bgziptabix/meta.yml index 5bef2350..92f62bf3 100644 --- a/modules/tabix/bgziptabix/meta.yml +++ b/modules/tabix/bgziptabix/meta.yml @@ -39,6 +39,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@maxulysse" diff --git a/modules/tabix/tabix/functions.nf b/modules/tabix/tabix/functions.nf index da9da093..85628ee0 100644 --- a/modules/tabix/tabix/functions.nf +++ b/modules/tabix/tabix/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/tabix/tabix/main.nf b/modules/tabix/tabix/main.nf index df1e84ee..f703a787 100644 --- a/modules/tabix/tabix/main.nf +++ b/modules/tabix/tabix/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process TABIX_TABIX { output: tuple val(meta), path("*.tbi"), emit: tbi - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) """ tabix $options.args $tab - echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//') + END_VERSIONS """ } diff --git a/modules/tabix/tabix/meta.yml b/modules/tabix/tabix/meta.yml index f66270db..1ca58bcf 100644 --- a/modules/tabix/tabix/meta.yml +++ b/modules/tabix/tabix/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/tiddit/sv/functions.nf b/modules/tiddit/sv/functions.nf index da9da093..85628ee0 100644 --- a/modules/tiddit/sv/functions.nf +++ b/modules/tiddit/sv/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf index bd42f7d1..b7fe1b03 100644 --- a/modules/tiddit/sv/main.nf +++ b/modules/tiddit/sv/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -27,7 +27,7 @@ process TIDDIT_SV { tuple val(meta), path("*.vcf") , emit: vcf tuple val(meta), path("*.ploidy.tab") , emit: ploidy tuple val(meta), path("*.signals.tab"), emit: signals - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -40,6 +40,9 @@ process TIDDIT_SV { $reference \\ -o $prefix - echo \$(tiddit -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(tiddit -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//') + END_VERSIONS """ } diff --git a/modules/tiddit/sv/meta.yml b/modules/tiddit/sv/meta.yml index f1601f72..2a351766 100644 --- a/modules/tiddit/sv/meta.yml +++ b/modules/tiddit/sv/meta.yml @@ -45,6 +45,6 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@maxulysse" diff --git a/modules/trimgalore/functions.nf b/modules/trimgalore/functions.nf index da9da093..85628ee0 100644 --- a/modules/trimgalore/functions.nf +++ b/modules/trimgalore/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/trimgalore/main.nf b/modules/trimgalore/main.nf index 3c16d66f..c002062a 100644 --- a/modules/trimgalore/main.nf +++ b/modules/trimgalore/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process TRIMGALORE { output: tuple val(meta), path("*.fq.gz") , emit: reads tuple val(meta), path("*report.txt"), emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version tuple val(meta), path("*.html"), emit: html optional true tuple val(meta), path("*.zip") , emit: zip optional true @@ -60,7 +60,10 @@ process TRIMGALORE { $c_r1 \\ $tpc_r1 \\ ${prefix}.fastq.gz - echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(trim_galore --version 2>&1 | sed 's/^.*version //; s/Last.*\$//') + END_VERSIONS """ } else { """ @@ -77,7 +80,10 @@ process TRIMGALORE { $tpc_r2 \\ ${prefix}_1.fastq.gz \\ ${prefix}_2.fastq.gz - echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(trim_galore --version 2>&1 | sed 's/^.*version //; s/Last.*\$//') + END_VERSIONS """ } } diff --git a/modules/trimgalore/meta.yml b/modules/trimgalore/meta.yml index 73538707..0c9fc925 100644 --- a/modules/trimgalore/meta.yml +++ b/modules/trimgalore/meta.yml @@ -51,7 +51,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/ucsc/bed12tobigbed/functions.nf b/modules/ucsc/bed12tobigbed/functions.nf index da9da093..85628ee0 100644 --- a/modules/ucsc/bed12tobigbed/functions.nf +++ b/modules/ucsc/bed12tobigbed/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/ucsc/bed12tobigbed/main.nf b/modules/ucsc/bed12tobigbed/main.nf index 407379fd..2f9b287b 100644 --- a/modules/ucsc/bed12tobigbed/main.nf +++ b/modules/ucsc/bed12tobigbed/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process UCSC_BED12TOBIGBED { output: tuple val(meta), path("*.bigBed"), emit: bigbed - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process UCSC_BED12TOBIGBED { $sizes \\ ${prefix}.bigBed - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/ucsc/bed12tobigbed/meta.yml b/modules/ucsc/bed12tobigbed/meta.yml index 7541eb2d..9bd2dd46 100755 --- a/modules/ucsc/bed12tobigbed/meta.yml +++ b/modules/ucsc/bed12tobigbed/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bigbed: type: file description: bigBed file diff --git a/modules/ucsc/bedclip/functions.nf b/modules/ucsc/bedclip/functions.nf index da9da093..85628ee0 100755 --- a/modules/ucsc/bedclip/functions.nf +++ b/modules/ucsc/bedclip/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/ucsc/bedclip/main.nf b/modules/ucsc/bedclip/main.nf index d1a47554..c001b410 100755 --- a/modules/ucsc/bedclip/main.nf +++ b/modules/ucsc/bedclip/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,7 +26,7 @@ process UCSC_BEDCLIP { output: tuple val(meta), path("*.bedGraph"), emit: bedgraph - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -37,6 +37,9 @@ process UCSC_BEDCLIP { $sizes \\ ${prefix}.bedGraph - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/ucsc/bedclip/meta.yml b/modules/ucsc/bedclip/meta.yml index f20b4617..b11d2083 100755 --- a/modules/ucsc/bedclip/meta.yml +++ b/modules/ucsc/bedclip/meta.yml @@ -31,7 +31,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bedgraph: type: file description: bedGraph file diff --git a/modules/ucsc/bedgraphtobigwig/functions.nf b/modules/ucsc/bedgraphtobigwig/functions.nf index da9da093..85628ee0 100644 --- a/modules/ucsc/bedgraphtobigwig/functions.nf +++ b/modules/ucsc/bedgraphtobigwig/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/ucsc/bedgraphtobigwig/main.nf b/modules/ucsc/bedgraphtobigwig/main.nf index e5fe3b7f..60e046f9 100644 --- a/modules/ucsc/bedgraphtobigwig/main.nf +++ b/modules/ucsc/bedgraphtobigwig/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -26,13 +26,16 @@ process UCSC_BEDGRAPHTOBIGWIG { output: tuple val(meta), path("*.bigWig"), emit: bigwig - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/ucsc/bedgraphtobigwig/meta.yml b/modules/ucsc/bedgraphtobigwig/meta.yml index 31365f48..ea20604c 100755 --- a/modules/ucsc/bedgraphtobigwig/meta.yml +++ b/modules/ucsc/bedgraphtobigwig/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bigwig: type: file description: bigWig file diff --git a/modules/ucsc/bigwigaverageoverbed/functions.nf b/modules/ucsc/bigwigaverageoverbed/functions.nf index da9da093..85628ee0 100755 --- a/modules/ucsc/bigwigaverageoverbed/functions.nf +++ b/modules/ucsc/bigwigaverageoverbed/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/ucsc/bigwigaverageoverbed/main.nf b/modules/ucsc/bigwigaverageoverbed/main.nf index 0aef3fca..adba3c76 100644 --- a/modules/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/ucsc/bigwigaverageoverbed/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process UCSC_BIGWIGAVERAGEOVERBED { output: tuple val(meta), path("*.tab") , emit: tab - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -33,6 +33,9 @@ process UCSC_BIGWIGAVERAGEOVERBED { # there is a bug that bigWigAverageOverBed can not handle ensembl seqlevels style. bigWigAverageOverBed ${options.args} $bigwig $bed ${bed.getSimpleName()}.tab - echo \$(bigWigAverageOverBed 2>&1) | sed 's/bigWigAverageOverBed v//; s/ - Compute.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(bigWigAverageOverBed 2>&1 | sed 's/bigWigAverageOverBed v//; s/ - Compute.*\$//') + END_VERSIONS """ } diff --git a/modules/ucsc/bigwigaverageoverbed/meta.yml b/modules/ucsc/bigwigaverageoverbed/meta.yml index 1f007f42..93328df0 100644 --- a/modules/ucsc/bigwigaverageoverbed/meta.yml +++ b/modules/ucsc/bigwigaverageoverbed/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - tab: type: file description: tab file diff --git a/modules/ucsc/wigtobigwig/functions.nf b/modules/ucsc/wigtobigwig/functions.nf index da9da093..85628ee0 100755 --- a/modules/ucsc/wigtobigwig/functions.nf +++ b/modules/ucsc/wigtobigwig/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/ucsc/wigtobigwig/main.nf b/modules/ucsc/wigtobigwig/main.nf index dee2d0bd..945f07c9 100644 --- a/modules/ucsc/wigtobigwig/main.nf +++ b/modules/ucsc/wigtobigwig/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process UCSC_WIGTOBIGWIG { output: path "*.bw" , emit: bw - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process UCSC_WIGTOBIGWIG { $chromsizes \\ ${wig.getSimpleName()}.bw - echo \$(wigToBigWig 2>&1) | sed 's/wigToBigWig v //; s/ - Convert.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(wigToBigWig 2>&1 | sed 's/wigToBigWig v //; s/ - Convert.*\$//') + END_VERSIONS """ } diff --git a/modules/ucsc/wigtobigwig/meta.yml b/modules/ucsc/wigtobigwig/meta.yml index 6ed4b026..102fd8ef 100644 --- a/modules/ucsc/wigtobigwig/meta.yml +++ b/modules/ucsc/wigtobigwig/meta.yml @@ -27,7 +27,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bw: type: file description: bigwig file diff --git a/modules/umitools/dedup/functions.nf b/modules/umitools/dedup/functions.nf index da9da093..85628ee0 100644 --- a/modules/umitools/dedup/functions.nf +++ b/modules/umitools/dedup/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/umitools/dedup/main.nf b/modules/umitools/dedup/main.nf index f30ab164..0f15c86c 100644 --- a/modules/umitools/dedup/main.nf +++ b/modules/umitools/dedup/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process UMITOOLS_DEDUP { output: tuple val(meta), path("*.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process UMITOOLS_DEDUP { $paired \\ $options.args - echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') + END_VERSIONS """ } diff --git a/modules/umitools/extract/functions.nf b/modules/umitools/extract/functions.nf index da9da093..85628ee0 100644 --- a/modules/umitools/extract/functions.nf +++ b/modules/umitools/extract/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/umitools/extract/main.nf b/modules/umitools/extract/main.nf index e5c4e21c..0a5e6636 100644 --- a/modules/umitools/extract/main.nf +++ b/modules/umitools/extract/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process UMITOOLS_EXTRACT { output: tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), path("*.log") , emit: log - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -38,7 +38,10 @@ process UMITOOLS_EXTRACT { $options.args \\ > ${prefix}.umi_extract.log - echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') + END_VERSIONS """ } else { """ @@ -51,7 +54,10 @@ process UMITOOLS_EXTRACT { $options.args \\ > ${prefix}.umi_extract.log - echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') + END_VERSIONS """ } } diff --git a/modules/unicycler/functions.nf b/modules/unicycler/functions.nf index da9da093..85628ee0 100644 --- a/modules/unicycler/functions.nf +++ b/modules/unicycler/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/unicycler/main.nf b/modules/unicycler/main.nf index 320c0f29..2b031c42 100644 --- a/modules/unicycler/main.nf +++ b/modules/unicycler/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process UNICYCLER { tuple val(meta), path('*.scaffolds.fa'), emit: scaffolds tuple val(meta), path('*.assembly.gfa'), emit: gfa tuple val(meta), path('*.log') , emit: log - path '*.version.txt' , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -42,6 +42,9 @@ process UNICYCLER { mv assembly.gfa ${prefix}.assembly.gfa mv unicycler.log ${prefix}.unicycler.log - echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(unicycler --version 2>&1 | sed 's/^.*Unicycler v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/unicycler/meta.yml b/modules/unicycler/meta.yml index 286b7f67..f6581919 100644 --- a/modules/unicycler/meta.yml +++ b/modules/unicycler/meta.yml @@ -33,7 +33,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - scaffolds: type: file description: Fasta file containing scaffolds @@ -49,7 +49,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@JoseEspinosa" - "@drpatelh" diff --git a/modules/untar/functions.nf b/modules/untar/functions.nf index da9da093..85628ee0 100644 --- a/modules/untar/functions.nf +++ b/modules/untar/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/untar/main.nf b/modules/untar/main.nf index fc6d7ec5..25b39904 100644 --- a/modules/untar/main.nf +++ b/modules/untar/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,13 +23,16 @@ process UNTAR { output: path "$untar" , emit: untar - path "*.version.txt", emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) untar = archive.toString() - '.tar.gz' """ tar -xzvf $options.args $archive - echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(tar --version 2>&1 | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') + END_VERSIONS """ } diff --git a/modules/untar/meta.yml b/modules/untar/meta.yml index af4674f0..0dc38292 100644 --- a/modules/untar/meta.yml +++ b/modules/untar/meta.yml @@ -21,7 +21,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/unzip/functions.nf b/modules/unzip/functions.nf index da9da093..85628ee0 100644 --- a/modules/unzip/functions.nf +++ b/modules/unzip/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/unzip/main.nf b/modules/unzip/main.nf index b52fbb04..a2fe2594 100644 --- a/modules/unzip/main.nf +++ b/modules/unzip/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process UNZIP { output: path "${archive.baseName}/" , emit: unzipped_archive - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -38,6 +38,9 @@ process UNZIP { $options.args \\ $archive - echo \$(7za --help) | grep Version | sed 's/.*p7zip Version//; s/(.*//' 1> ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + 7za: \$( 7za --help) grep Version | sed 's/.*p7zip Version//; s/(.*//' ) + END_VERSIONS """ } diff --git a/modules/unzip/meta.yml b/modules/unzip/meta.yml index 97b1f1fc..386ca8bb 100644 --- a/modules/unzip/meta.yml +++ b/modules/unzip/meta.yml @@ -21,7 +21,7 @@ output: - version: type: file description: File or directory of decompressed archive - pattern: "*.{version.txt}" + pattern: "versions.yml" - unzipped_archive: type: directory description: Directory contents of the unzipped archive diff --git a/modules/variantbam/functions.nf b/modules/variantbam/functions.nf index da9da093..85628ee0 100644 --- a/modules/variantbam/functions.nf +++ b/modules/variantbam/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/variantbam/main.nf b/modules/variantbam/main.nf index dc29de58..c4ac3742 100644 --- a/modules/variantbam/main.nf +++ b/modules/variantbam/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -25,7 +25,7 @@ process VARIANTBAM { output: tuple val(meta), path("*.bam") , emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -36,6 +36,9 @@ process VARIANTBAM { -o ${prefix}.bam \\ $options.args - echo $VERSION > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS """ } diff --git a/modules/variantbam/meta.yml b/modules/variantbam/meta.yml index da0ff5e0..62ddb578 100644 --- a/modules/variantbam/meta.yml +++ b/modules/variantbam/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: Filtered or downsampled BAM file diff --git a/modules/vcftools/functions.nf b/modules/vcftools/functions.nf index da9da093..85628ee0 100644 --- a/modules/vcftools/functions.nf +++ b/modules/vcftools/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/vcftools/main.nf b/modules/vcftools/main.nf index a0d8cd5a..7ae1619f 100644 --- a/modules/vcftools/main.nf +++ b/modules/vcftools/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -28,7 +28,7 @@ process VCFTOOLS { path(diff_variant_file) output: - path("*.version.txt"), emit: version + path("versions.yml") , emit: version tuple val(meta), path("*.vcf"), optional:true, emit: vcf tuple val(meta), path("*.bcf"), optional:true, emit: bcf @@ -124,6 +124,9 @@ process VCFTOOLS { $bed_arg \\ $diff_variant_arg \\ - echo \$(vcftools --version 2>&1) | sed 's/^.*vcftools //; s/Using.*\$//' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(vcftools --version 2>&1 | sed 's/^.*vcftools //; s/Using.*\$//') + END_VERSIONS """ } diff --git a/modules/vcftools/meta.yml b/modules/vcftools/meta.yml index 4da9b6c2..e39a0347 100644 --- a/modules/vcftools/meta.yml +++ b/modules/vcftools/meta.yml @@ -36,7 +36,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - vcf: type: file description: vcf file (optional) diff --git a/modules/yara/index/functions.nf b/modules/yara/index/functions.nf index da9da093..85628ee0 100644 --- a/modules/yara/index/functions.nf +++ b/modules/yara/index/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/yara/index/main.nf b/modules/yara/index/main.nf index f1fe13a5..c621e866 100644 --- a/modules/yara/index/main.nf +++ b/modules/yara/index/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -23,7 +23,7 @@ process YARA_INDEX { output: path "yara", emit: index - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,6 +34,9 @@ process YARA_INDEX { mv *.{lf,rid,sa,txt}.* yara cp $fasta yara/yara.fasta - echo \$(yara_indexer --help 2>&1) | grep -e "yara_indexer version:" | sed 's/yara_indexer version: //g' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(yara_indexer --help 2>&1 | grep -e "yara_indexer version:" | sed 's/yara_indexer version: //g') + END_VERSIONS """ } diff --git a/modules/yara/index/meta.yml b/modules/yara/index/meta.yml index f1e2ab93..acf70f2b 100644 --- a/modules/yara/index/meta.yml +++ b/modules/yara/index/meta.yml @@ -24,7 +24,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - index: type: file description: YARA genome index files diff --git a/modules/yara/mapper/functions.nf b/modules/yara/mapper/functions.nf index da9da093..85628ee0 100644 --- a/modules/yara/mapper/functions.nf +++ b/modules/yara/mapper/functions.nf @@ -9,6 +9,13 @@ def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // @@ -37,32 +44,35 @@ def getPathFromList(path_list) { // Function to save/publish module results // def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } + path = path instanceof String ? path : '' + path_list.add(path) } } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" } } diff --git a/modules/yara/mapper/main.nf b/modules/yara/mapper/main.nf index f888ae14..3404d591 100644 --- a/modules/yara/mapper/main.nf +++ b/modules/yara/mapper/main.nf @@ -1,5 +1,5 @@ // Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) @@ -24,7 +24,7 @@ process YARA_MAPPER { output: tuple val(meta), path("*.mapped.bam"), emit: bam - path "*.version.txt" , emit: version + path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) @@ -34,14 +34,20 @@ process YARA_MAPPER { """ yara_mapper $options.args -t ${task.cpus} -f bam ${index}/yara $reads | samtools view -@ ${task.cpus} -hb -F4 > ${prefix}.mapped.bam - echo \$(yara_mapper --help 2>&1) > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(yara_mapper --help 2>&1) + END_VERSIONS """ } else { """ yara_mapper $options.args -t ${task.cpus} -f bam ${index}/yara ${reads[0]} ${reads[1]} > output.bam samtools view -@ ${task.cpus} -hF 4 -f 0x40 -b output.bam > ${prefix}_1.mapped.bam samtools view -@ ${task.cpus} -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam - echo \$(yara_mapper --version 2>&1) | grep -e "yara_mapper version:" | sed 's/yara_mapper version: //g' > ${software}.version.txt + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(yara_mapper --version 2>&1 | grep -e "yara_mapper version:" | sed 's/yara_mapper version: //g') + END_VERSIONS """ } diff --git a/modules/yara/mapper/meta.yml b/modules/yara/mapper/meta.yml index 4a8e6494..4beb0c78 100644 --- a/modules/yara/mapper/meta.yml +++ b/modules/yara/mapper/meta.yml @@ -37,7 +37,7 @@ output: - version: type: file description: File containing software version - pattern: "*.{version.txt}" + pattern: "versions.yml" - bam: type: file description: Sorted BAM file