diff --git a/modules/abacas/main.nf b/modules/abacas/main.nf index 307e17d2..bc5440b1 100644 --- a/modules/abacas/main.nf +++ b/modules/abacas/main.nf @@ -24,10 +24,9 @@ process ABACAS { output: tuple val(meta), path('*.abacas*'), emit: results - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ abacas.pl \\ diff --git a/modules/adapterremoval/main.nf b/modules/adapterremoval/main.nf index cbf0957a..fad3963f 100644 --- a/modules/adapterremoval/main.nf +++ b/modules/adapterremoval/main.nf @@ -23,10 +23,9 @@ process ADAPTERREMOVAL { output: tuple val(meta), path('*.fastq.gz'), emit: reads tuple val(meta), path('*.log') , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { diff --git a/modules/agrvate/main.nf b/modules/agrvate/main.nf index 3ca2e0f4..c1a6748e 100644 --- a/modules/agrvate/main.nf +++ b/modules/agrvate/main.nf @@ -24,10 +24,9 @@ process AGRVATE { output: tuple val(meta), path("${fasta.baseName}-results/${fasta.baseName}-summary.tab"), emit: summary path "${fasta.baseName}-results" , emit: results_dir - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ agrvate \\ diff --git a/modules/allelecounter/main.nf b/modules/allelecounter/main.nf index 31ef3f79..5184df7d 100644 --- a/modules/allelecounter/main.nf +++ b/modules/allelecounter/main.nf @@ -24,10 +24,9 @@ process ALLELECOUNTER { output: tuple val(meta), path("*.alleleCount"), emit: allelecount - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ alleleCounter \\ diff --git a/modules/amps/main.nf b/modules/amps/main.nf index 676435f1..f34423b5 100644 --- a/modules/amps/main.nf +++ b/modules/amps/main.nf @@ -27,7 +27,7 @@ process AMPS { path "results/heatmap_overview_Wevid.pdf" , emit: summary_pdf path "results/heatmap_overview_Wevid.tsv" , emit: tsv path "results/pdf_candidate_profiles/" , emit: candidate_pdfs - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: """ @@ -41,7 +41,7 @@ process AMPS { cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: - amps: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//') + ${getSoftwareName(task.process)}: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//') END_VERSIONS """ } diff --git a/modules/arriba/main.nf b/modules/arriba/main.nf index b94c22d9..6abae233 100644 --- a/modules/arriba/main.nf +++ b/modules/arriba/main.nf @@ -26,10 +26,9 @@ process ARRIBA { output: tuple val(meta), path("*.fusions.tsv") , emit: fusions tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def blacklist = (options.args.contains('-b')) ? '' : '-f blacklist' """ diff --git a/modules/artic/guppyplex/main.nf b/modules/artic/guppyplex/main.nf index 5f91e9e3..87bd99c8 100644 --- a/modules/artic/guppyplex/main.nf +++ b/modules/artic/guppyplex/main.nf @@ -23,10 +23,9 @@ process ARTIC_GUPPYPLEX { output: tuple val(meta), path("*.fastq.gz"), emit: fastq - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ artic \\ diff --git a/modules/artic/minion/main.nf b/modules/artic/minion/main.nf index 2f810ecf..68474f19 100644 --- a/modules/artic/minion/main.nf +++ b/modules/artic/minion/main.nf @@ -40,10 +40,9 @@ process ARTIC_MINION { tuple val(meta), path("${prefix}.pass.vcf.gz") , emit: vcf tuple val(meta), path("${prefix}.pass.vcf.gz.tbi") , emit: tbi tuple val(meta), path("*.json"), optional:true , emit: json - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def version = scheme_version.toString().toLowerCase().replaceAll('v','') def fast5 = params.fast5_dir ? "--fast5-directory $fast5_dir" : "" diff --git a/modules/bamaligncleaner/main.nf b/modules/bamaligncleaner/main.nf index 7372f274..720b495a 100644 --- a/modules/bamaligncleaner/main.nf +++ b/modules/bamaligncleaner/main.nf @@ -23,10 +23,9 @@ process BAMALIGNCLEANER { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ diff --git a/modules/bandage/image/main.nf b/modules/bandage/image/main.nf index d15d4826..b7a30a0b 100644 --- a/modules/bandage/image/main.nf +++ b/modules/bandage/image/main.nf @@ -24,10 +24,9 @@ process BANDAGE_IMAGE { output: tuple val(meta), path('*.png'), emit: png tuple val(meta), path('*.svg'), emit: svg - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ Bandage image $gfa ${prefix}.png $options.args diff --git a/modules/bbmap/align/main.nf b/modules/bbmap/align/main.nf index 63989be0..733fd4d5 100644 --- a/modules/bbmap/align/main.nf +++ b/modules/bbmap/align/main.nf @@ -24,10 +24,9 @@ process BBMAP_ALIGN { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}" diff --git a/modules/bbmap/bbduk/main.nf b/modules/bbmap/bbduk/main.nf index 4f1540dc..d7243fdb 100644 --- a/modules/bbmap/bbduk/main.nf +++ b/modules/bbmap/bbduk/main.nf @@ -24,10 +24,9 @@ process BBMAP_BBDUK { output: tuple val(meta), path('*.fastq.gz'), emit: reads tuple val(meta), path('*.log') , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}" def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz" diff --git a/modules/bbmap/bbsplit/main.nf b/modules/bbmap/bbsplit/main.nf index 614a4c02..7a24312b 100644 --- a/modules/bbmap/bbsplit/main.nf +++ b/modules/bbmap/bbsplit/main.nf @@ -30,10 +30,9 @@ process BBMAP_BBSPLIT { tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq tuple val(meta), path('*fastq.gz') , optional:true, emit: all_fastq tuple val(meta), path('*txt') , optional:true, emit: stats - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def avail_mem = 3 diff --git a/modules/bbmap/index/main.nf b/modules/bbmap/index/main.nf index 6f957d03..b9e52ec7 100644 --- a/modules/bbmap/index/main.nf +++ b/modules/bbmap/index/main.nf @@ -23,10 +23,9 @@ process BBMAP_INDEX { output: path 'ref' , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ bbmap.sh \\ ref=${fasta} \\ diff --git a/modules/bcftools/concat/main.nf b/modules/bcftools/concat/main.nf index fab0e83d..48280eea 100644 --- a/modules/bcftools/concat/main.nf +++ b/modules/bcftools/concat/main.nf @@ -23,10 +23,9 @@ process BCFTOOLS_CONCAT { output: tuple val(meta), path("*.gz"), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bcftools concat \\ diff --git a/modules/bcftools/consensus/main.nf b/modules/bcftools/consensus/main.nf index 29758a4b..954b0eb8 100644 --- a/modules/bcftools/consensus/main.nf +++ b/modules/bcftools/consensus/main.nf @@ -23,10 +23,9 @@ process BCFTOOLS_CONSENSUS { output: tuple val(meta), path('*.fa'), emit: fasta - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ cat $fasta | bcftools consensus $vcf $options.args > ${prefix}.fa diff --git a/modules/bcftools/filter/main.nf b/modules/bcftools/filter/main.nf index 37b7e28b..5323e0fb 100644 --- a/modules/bcftools/filter/main.nf +++ b/modules/bcftools/filter/main.nf @@ -23,10 +23,9 @@ process BCFTOOLS_FILTER { output: tuple val(meta), path("*.gz"), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bcftools filter \\ diff --git a/modules/bcftools/isec/main.nf b/modules/bcftools/isec/main.nf index f700f35c..cc3e425e 100644 --- a/modules/bcftools/isec/main.nf +++ b/modules/bcftools/isec/main.nf @@ -23,10 +23,9 @@ process BCFTOOLS_ISEC { output: tuple val(meta), path("${prefix}"), emit: results - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bcftools isec \\ diff --git a/modules/bcftools/merge/main.nf b/modules/bcftools/merge/main.nf index 7d8ab670..bb68f184 100644 --- a/modules/bcftools/merge/main.nf +++ b/modules/bcftools/merge/main.nf @@ -23,10 +23,9 @@ process BCFTOOLS_MERGE { output: tuple val(meta), path("*.gz"), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bcftools merge -Oz \\ diff --git a/modules/bcftools/mpileup/main.nf b/modules/bcftools/mpileup/main.nf index 1f6eecaa..df8455a5 100644 --- a/modules/bcftools/mpileup/main.nf +++ b/modules/bcftools/mpileup/main.nf @@ -26,10 +26,9 @@ process BCFTOOLS_MPILEUP { tuple val(meta), path("*.gz") , emit: vcf tuple val(meta), path("*.tbi") , emit: tbi tuple val(meta), path("*stats.txt"), emit: stats - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ echo "${meta.id}" > sample_name.list diff --git a/modules/bcftools/norm/main.nf b/modules/bcftools/norm/main.nf index 454fc1d2..7e506e49 100644 --- a/modules/bcftools/norm/main.nf +++ b/modules/bcftools/norm/main.nf @@ -24,10 +24,9 @@ process BCFTOOLS_NORM { output: tuple val(meta), path("*.gz") , emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bcftools norm \\ diff --git a/modules/bcftools/query/main.nf b/modules/bcftools/query/main.nf index 4815ae90..dae8bbc4 100644 --- a/modules/bcftools/query/main.nf +++ b/modules/bcftools/query/main.nf @@ -26,10 +26,9 @@ process BCFTOOLS_QUERY { output: tuple val(meta), path("*.gz") , emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def regions_file = regions ? "--regions-file ${regions}" : "" def targets_file = targets ? "--targets-file ${targets}" : "" diff --git a/modules/bcftools/reheader/main.nf b/modules/bcftools/reheader/main.nf index a949b6e9..953a8adb 100644 --- a/modules/bcftools/reheader/main.nf +++ b/modules/bcftools/reheader/main.nf @@ -25,10 +25,9 @@ process BCFTOOLS_REHEADER { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def update_sequences = fai ? "-f $fai" : "" def new_header = header ? "-h $header" : "" diff --git a/modules/bcftools/stats/main.nf b/modules/bcftools/stats/main.nf index f5b1f6b1..31bed814 100644 --- a/modules/bcftools/stats/main.nf +++ b/modules/bcftools/stats/main.nf @@ -23,10 +23,9 @@ process BCFTOOLS_STATS { output: tuple val(meta), path("*stats.txt"), emit: stats - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bcftools stats $options.args $vcf > ${prefix}.bcftools_stats.txt diff --git a/modules/bcftools/view/main.nf b/modules/bcftools/view/main.nf index 5a944e89..ef72f081 100644 --- a/modules/bcftools/view/main.nf +++ b/modules/bcftools/view/main.nf @@ -26,10 +26,9 @@ process BCFTOOLS_VIEW { output: tuple val(meta), path("*.gz") , emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def regions_file = regions ? "--regions-file ${regions}" : "" def targets_file = targets ? "--targets-file ${targets}" : "" diff --git a/modules/bedtools/bamtobed/main.nf b/modules/bedtools/bamtobed/main.nf index 19986371..71c439d3 100644 --- a/modules/bedtools/bamtobed/main.nf +++ b/modules/bedtools/bamtobed/main.nf @@ -23,10 +23,9 @@ process BEDTOOLS_BAMTOBED { output: tuple val(meta), path("*.bed"), emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedtools \\ diff --git a/modules/bedtools/complement/main.nf b/modules/bedtools/complement/main.nf index 5b3bbea9..77214c64 100644 --- a/modules/bedtools/complement/main.nf +++ b/modules/bedtools/complement/main.nf @@ -24,10 +24,9 @@ process BEDTOOLS_COMPLEMENT { output: tuple val(meta), path('*.bed'), emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedtools \\ diff --git a/modules/bedtools/genomecov/main.nf b/modules/bedtools/genomecov/main.nf index b5deedf1..9d014466 100644 --- a/modules/bedtools/genomecov/main.nf +++ b/modules/bedtools/genomecov/main.nf @@ -25,10 +25,9 @@ process BEDTOOLS_GENOMECOV { output: tuple val(meta), path("*.${extension}"), emit: genomecov - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (intervals.name =~ /\.bam/) { """ diff --git a/modules/bedtools/getfasta/main.nf b/modules/bedtools/getfasta/main.nf index 72e457dc..b27f6183 100644 --- a/modules/bedtools/getfasta/main.nf +++ b/modules/bedtools/getfasta/main.nf @@ -24,10 +24,9 @@ process BEDTOOLS_GETFASTA { output: path "*.fa" , emit: fasta - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${bed.baseName}${options.suffix}" : "${bed.baseName}" """ bedtools \\ diff --git a/modules/bedtools/intersect/main.nf b/modules/bedtools/intersect/main.nf index b75bd116..1ab0a8b2 100644 --- a/modules/bedtools/intersect/main.nf +++ b/modules/bedtools/intersect/main.nf @@ -24,10 +24,9 @@ process BEDTOOLS_INTERSECT { output: tuple val(meta), path("*.${extension}"), emit: intersect - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedtools \\ diff --git a/modules/bedtools/makewindows/main.nf b/modules/bedtools/makewindows/main.nf index 5e93f0ae..c9f863d0 100644 --- a/modules/bedtools/makewindows/main.nf +++ b/modules/bedtools/makewindows/main.nf @@ -24,10 +24,9 @@ process BEDTOOLS_MAKEWINDOWS { output: tuple val(meta), path("*.tab"), emit: tab - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def arg_input = use_bed ? "-b $regions" : "-g $regions" """ diff --git a/modules/bedtools/maskfasta/main.nf b/modules/bedtools/maskfasta/main.nf index 67097f3f..8ee33d7a 100644 --- a/modules/bedtools/maskfasta/main.nf +++ b/modules/bedtools/maskfasta/main.nf @@ -24,10 +24,9 @@ process BEDTOOLS_MASKFASTA { output: tuple val(meta), path("*.fa"), emit: fasta - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedtools \\ diff --git a/modules/bedtools/merge/main.nf b/modules/bedtools/merge/main.nf index ba8348af..92a59f9e 100644 --- a/modules/bedtools/merge/main.nf +++ b/modules/bedtools/merge/main.nf @@ -23,10 +23,9 @@ process BEDTOOLS_MERGE { output: tuple val(meta), path('*.bed'), emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedtools \\ diff --git a/modules/bedtools/slop/main.nf b/modules/bedtools/slop/main.nf index 6644b8db..4b412b1f 100644 --- a/modules/bedtools/slop/main.nf +++ b/modules/bedtools/slop/main.nf @@ -24,10 +24,9 @@ process BEDTOOLS_SLOP { output: tuple val(meta), path("*.bed"), emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedtools \\ diff --git a/modules/bedtools/sort/main.nf b/modules/bedtools/sort/main.nf index acc4a593..bdba3376 100644 --- a/modules/bedtools/sort/main.nf +++ b/modules/bedtools/sort/main.nf @@ -23,10 +23,9 @@ process BEDTOOLS_SORT { output: tuple val(meta), path('*.bed'), emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedtools \\ diff --git a/modules/bedtools/subtract/main.nf b/modules/bedtools/subtract/main.nf index a8e2ad02..54a12bf4 100644 --- a/modules/bedtools/subtract/main.nf +++ b/modules/bedtools/subtract/main.nf @@ -23,10 +23,9 @@ process BEDTOOLS_SUBTRACT { output: tuple val(meta), path("*.bed"), emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedtools \\ diff --git a/modules/bismark/align/main.nf b/modules/bismark/align/main.nf index ce042933..aa4879ba 100644 --- a/modules/bismark/align/main.nf +++ b/modules/bismark/align/main.nf @@ -26,10 +26,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def fastq = meta.single_end ? reads : "-1 ${reads[0]} -2 ${reads[1]}" """ diff --git a/modules/bismark/deduplicate/main.nf b/modules/bismark/deduplicate/main.nf index 8555563d..c3ff27d6 100644 --- a/modules/bismark/deduplicate/main.nf +++ b/modules/bismark/deduplicate/main.nf @@ -24,10 +24,9 @@ process BISMARK_DEDUPLICATE { output: tuple val(meta), path("*.deduplicated.bam") , emit: bam tuple val(meta), path("*.deduplication_report.txt"), emit: report - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def seqtype = meta.single_end ? '-s' : '-p' """ diff --git a/modules/bismark/genomepreparation/main.nf b/modules/bismark/genomepreparation/main.nf index 0a3fae14..0a86173d 100644 --- a/modules/bismark/genomepreparation/main.nf +++ b/modules/bismark/genomepreparation/main.nf @@ -23,10 +23,9 @@ process BISMARK_GENOMEPREPARATION { output: path "BismarkIndex" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ bismark_genome_preparation \\ $options.args \\ diff --git a/modules/bismark/methylationextractor/main.nf b/modules/bismark/methylationextractor/main.nf index bafeaad6..5e89e6f8 100644 --- a/modules/bismark/methylationextractor/main.nf +++ b/modules/bismark/methylationextractor/main.nf @@ -28,11 +28,10 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: def seqtype = meta.single_end ? '-s' : '-p' - def software = getSoftwareName(task.process) """ bismark_methylation_extractor \\ --bedGraph \\ diff --git a/modules/bismark/report/main.nf b/modules/bismark/report/main.nf index d7ab3e01..70c6ba3b 100644 --- a/modules/bismark/report/main.nf +++ b/modules/bismark/report/main.nf @@ -23,10 +23,9 @@ process BISMARK_REPORT { output: tuple val(meta), path("*report.{html,txt}"), emit: report - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ bismark2report $options.args diff --git a/modules/bismark/summary/main.nf b/modules/bismark/summary/main.nf index d71772b3..3d5f294e 100644 --- a/modules/bismark/summary/main.nf +++ b/modules/bismark/summary/main.nf @@ -26,10 +26,9 @@ process BISMARK_SUMMARY { output: path "*report.{html,txt}", emit: summary - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ bismark2summary diff --git a/modules/blast/blastn/main.nf b/modules/blast/blastn/main.nf index 1146ede4..0d65f1d0 100644 --- a/modules/blast/blastn/main.nf +++ b/modules/blast/blastn/main.nf @@ -24,10 +24,9 @@ process BLAST_BLASTN { output: tuple val(meta), path('*.blastn.txt'), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'` diff --git a/modules/blast/makeblastdb/main.nf b/modules/blast/makeblastdb/main.nf index 9ee02108..0538e0db 100644 --- a/modules/blast/makeblastdb/main.nf +++ b/modules/blast/makeblastdb/main.nf @@ -23,10 +23,9 @@ process BLAST_MAKEBLASTDB { output: path 'blast_db' , emit: db - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ makeblastdb \\ -in $fasta \\ diff --git a/modules/bowtie/align/main.nf b/modules/bowtie/align/main.nf index 7c71cb82..764b5be2 100644 --- a/modules/bowtie/align/main.nf +++ b/modules/bowtie/align/main.nf @@ -25,11 +25,10 @@ process BOWTIE_ALIGN { output: tuple val(meta), path('*.bam'), emit: bam tuple val(meta), path('*.out'), emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : '' def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}" diff --git a/modules/bowtie/build/main.nf b/modules/bowtie/build/main.nf index 3ae07729..1b83541b 100644 --- a/modules/bowtie/build/main.nf +++ b/modules/bowtie/build/main.nf @@ -23,10 +23,9 @@ process BOWTIE_BUILD { output: path 'bowtie' , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ mkdir bowtie bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName} diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf index 4a972373..6f923951 100644 --- a/modules/bowtie2/align/main.nf +++ b/modules/bowtie2/align/main.nf @@ -25,11 +25,10 @@ process BOWTIE2_ALIGN { output: tuple val(meta), path('*.bam'), emit: bam tuple val(meta), path('*.log'), emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' diff --git a/modules/bowtie2/build/main.nf b/modules/bowtie2/build/main.nf index f140d7a4..bc95eea8 100644 --- a/modules/bowtie2/build/main.nf +++ b/modules/bowtie2/build/main.nf @@ -23,10 +23,9 @@ process BOWTIE2_BUILD { output: path 'bowtie2' , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ mkdir bowtie2 bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName} diff --git a/modules/bwa/aln/main.nf b/modules/bwa/aln/main.nf index ae4ee147..07135aea 100644 --- a/modules/bwa/aln/main.nf +++ b/modules/bwa/aln/main.nf @@ -24,10 +24,9 @@ process BWA_ALN { output: tuple val(meta), path("*.sai"), emit: sai - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { diff --git a/modules/bwa/index/main.nf b/modules/bwa/index/main.nf index 9de3fe0c..479431ed 100644 --- a/modules/bwa/index/main.nf +++ b/modules/bwa/index/main.nf @@ -23,10 +23,9 @@ process BWA_INDEX { output: path "bwa" , emit: index - path "versions.yml", emit: version + path "versions.yml", emit: versions script: - def software = getSoftwareName(task.process) """ mkdir bwa bwa \\ diff --git a/modules/bwa/mem/main.nf b/modules/bwa/mem/main.nf index f20e0c39..b6a548d7 100644 --- a/modules/bwa/mem/main.nf +++ b/modules/bwa/mem/main.nf @@ -24,10 +24,9 @@ process BWA_MEM { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" """ diff --git a/modules/bwa/sampe/main.nf b/modules/bwa/sampe/main.nf index f4519541..38127793 100644 --- a/modules/bwa/sampe/main.nf +++ b/modules/bwa/sampe/main.nf @@ -24,10 +24,9 @@ process BWA_SAMPE { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def read_group = meta.read_group ? "-r ${meta.read_group}" : "" diff --git a/modules/bwa/samse/main.nf b/modules/bwa/samse/main.nf index 5303b24f..68fa95c7 100644 --- a/modules/bwa/samse/main.nf +++ b/modules/bwa/samse/main.nf @@ -24,10 +24,9 @@ process BWA_SAMSE { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def read_group = meta.read_group ? "-r ${meta.read_group}" : "" diff --git a/modules/bwamem2/index/main.nf b/modules/bwamem2/index/main.nf index 9274ebe8..5732017f 100644 --- a/modules/bwamem2/index/main.nf +++ b/modules/bwamem2/index/main.nf @@ -23,10 +23,9 @@ process BWAMEM2_INDEX { output: path "bwamem2" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ mkdir bwamem2 bwa-mem2 \\ diff --git a/modules/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf index ea584a39..f88d840f 100644 --- a/modules/bwamem2/mem/main.nf +++ b/modules/bwamem2/mem/main.nf @@ -24,10 +24,9 @@ process BWAMEM2_MEM { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" """ diff --git a/modules/bwameth/align/main.nf b/modules/bwameth/align/main.nf index d78055fc..9b1d2b86 100644 --- a/modules/bwameth/align/main.nf +++ b/modules/bwameth/align/main.nf @@ -24,10 +24,9 @@ process BWAMETH_ALIGN { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" """ diff --git a/modules/bwameth/index/main.nf b/modules/bwameth/index/main.nf index a7a0b783..68fb33d4 100644 --- a/modules/bwameth/index/main.nf +++ b/modules/bwameth/index/main.nf @@ -23,10 +23,9 @@ process BWAMETH_INDEX { output: path "bwameth" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ bwameth.py index $fasta diff --git a/modules/cat/cat/main.nf b/modules/cat/cat/main.nf index 2dc9944f..dac301cb 100644 --- a/modules/cat/cat/main.nf +++ b/modules/cat/cat/main.nf @@ -23,7 +23,7 @@ process CAT_CAT { output: path "${file_out}*" , emit: file_out - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: def file_list = files_in.collect { it.toString() } diff --git a/modules/cat/fastq/main.nf b/modules/cat/fastq/main.nf index 712364e1..538915a7 100644 --- a/modules/cat/fastq/main.nf +++ b/modules/cat/fastq/main.nf @@ -23,7 +23,7 @@ process CAT_FASTQ { output: tuple val(meta), path("*.merged.fastq.gz"), emit: reads - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" diff --git a/modules/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf index c7b0a5a3..9826eed1 100644 --- a/modules/chromap/chromap/main.nf +++ b/modules/chromap/chromap/main.nf @@ -34,10 +34,9 @@ process CHROMAP_CHROMAP { tuple val(meta), path("*.bam") , optional:true, emit: bam tuple val(meta), path("*.tagAlign.gz"), optional:true, emit: tagAlign tuple val(meta), path("*.pairs.gz") , optional:true, emit: pairs - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def args = options.args.tokenize() diff --git a/modules/chromap/index/main.nf b/modules/chromap/index/main.nf index 61b7a856..efe85733 100644 --- a/modules/chromap/index/main.nf +++ b/modules/chromap/index/main.nf @@ -25,10 +25,9 @@ process CHROMAP_INDEX { output: path "*.index" , emit: index - path "versions.yml", emit: version + path "versions.yml", emit: versions script: - def software = getSoftwareName(task.process) def prefix = fasta.baseName """ chromap \\ diff --git a/modules/cnvkit/main.nf b/modules/cnvkit/main.nf index 1219584c..27c8bb0d 100755 --- a/modules/cnvkit/main.nf +++ b/modules/cnvkit/main.nf @@ -28,10 +28,9 @@ process CNVKIT { tuple val(meta), path("*.cnn"), emit: cnn tuple val(meta), path("*.cnr"), emit: cnr tuple val(meta), path("*.cns"), emit: cns - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ cnvkit.py \\ batch \\ diff --git a/modules/cooler/digest/main.nf b/modules/cooler/digest/main.nf index ee8b347e..5728b649 100644 --- a/modules/cooler/digest/main.nf +++ b/modules/cooler/digest/main.nf @@ -25,10 +25,9 @@ process COOLER_DIGEST { output: path "*.bed" , emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ cooler digest \\ $options.args \\ diff --git a/modules/cooler/dump/main.nf b/modules/cooler/dump/main.nf index 7d456107..2028f5f0 100644 --- a/modules/cooler/dump/main.nf +++ b/modules/cooler/dump/main.nf @@ -23,10 +23,9 @@ process COOLER_DUMP { output: tuple val(meta), path("*.bedpe"), emit: bedpe - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ cooler dump \\ diff --git a/modules/custom/dumpsoftwareversions/main.nf b/modules/custom/dumpsoftwareversions/main.nf index 8424ab07..cf10a8e0 100644 --- a/modules/custom/dumpsoftwareversions/main.nf +++ b/modules/custom/dumpsoftwareversions/main.nf @@ -22,9 +22,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { path versions output: - path 'software_versions.yml' , emit: yml - path 'software_versions_mqc.yml', emit: mqc_yml - path 'versions.yml' , emit: versions + path "software_versions.yml" , emit: yml + path "software_versions_mqc.yml", emit: mqc_yml + path "versions.yml" , emit: versions script: """ diff --git a/modules/cutadapt/main.nf b/modules/cutadapt/main.nf index 3baf9c7f..32faf2cf 100644 --- a/modules/cutadapt/main.nf +++ b/modules/cutadapt/main.nf @@ -24,10 +24,9 @@ process CUTADAPT { output: tuple val(meta), path('*.trim.fastq.gz'), emit: reads tuple val(meta), path('*.log') , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def trimmed = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz" """ diff --git a/modules/damageprofiler/main.nf b/modules/damageprofiler/main.nf index cbb27944..1537b019 100644 --- a/modules/damageprofiler/main.nf +++ b/modules/damageprofiler/main.nf @@ -25,10 +25,9 @@ process DAMAGEPROFILER { output: tuple val(meta), path("${prefix}"), emit: results - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ diff --git a/modules/deeptools/computematrix/main.nf b/modules/deeptools/computematrix/main.nf index 21a18526..9fffdb8e 100644 --- a/modules/deeptools/computematrix/main.nf +++ b/modules/deeptools/computematrix/main.nf @@ -25,10 +25,9 @@ process DEEPTOOLS_COMPUTEMATRIX { output: tuple val(meta), path("*.mat.gz") , emit: matrix tuple val(meta), path("*.mat.tab"), emit: table - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ computeMatrix \\ diff --git a/modules/deeptools/plotfingerprint/main.nf b/modules/deeptools/plotfingerprint/main.nf index 9271a399..b2d167f9 100644 --- a/modules/deeptools/plotfingerprint/main.nf +++ b/modules/deeptools/plotfingerprint/main.nf @@ -25,10 +25,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def extend = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : '' """ diff --git a/modules/deeptools/plotheatmap/main.nf b/modules/deeptools/plotheatmap/main.nf index 49362666..19c243df 100644 --- a/modules/deeptools/plotheatmap/main.nf +++ b/modules/deeptools/plotheatmap/main.nf @@ -24,10 +24,9 @@ process DEEPTOOLS_PLOTHEATMAP { output: tuple val(meta), path("*.pdf"), emit: pdf tuple val(meta), path("*.tab"), emit: table - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ plotHeatmap \\ diff --git a/modules/deeptools/plotprofile/main.nf b/modules/deeptools/plotprofile/main.nf index cba8e161..3a196bd5 100644 --- a/modules/deeptools/plotprofile/main.nf +++ b/modules/deeptools/plotprofile/main.nf @@ -24,10 +24,9 @@ process DEEPTOOLS_PLOTPROFILE { output: tuple val(meta), path("*.pdf"), emit: pdf tuple val(meta), path("*.tab"), emit: table - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ plotProfile \\ diff --git a/modules/delly/call/main.nf b/modules/delly/call/main.nf index 0688949e..59979dc9 100644 --- a/modules/delly/call/main.nf +++ b/modules/delly/call/main.nf @@ -26,10 +26,9 @@ process DELLY_CALL { output: tuple val(meta), path("*.bcf"), emit: bcf tuple val(meta), path("*.csi"), emit: csi - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ delly \\ diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf index 556f150c..6afc66c4 100644 --- a/modules/diamond/blastp/main.nf +++ b/modules/diamond/blastp/main.nf @@ -26,10 +26,9 @@ process DIAMOND_BLASTP { output: tuple val(meta), path('*.txt'), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf index 8b0227a2..db2953da 100644 --- a/modules/diamond/blastx/main.nf +++ b/modules/diamond/blastx/main.nf @@ -26,10 +26,9 @@ process DIAMOND_BLASTX { output: tuple val(meta), path('*.txt'), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` diff --git a/modules/diamond/makedb/main.nf b/modules/diamond/makedb/main.nf index 27383955..e4533f8f 100644 --- a/modules/diamond/makedb/main.nf +++ b/modules/diamond/makedb/main.nf @@ -25,10 +25,9 @@ process DIAMOND_MAKEDB { output: path "${fasta}.dmnd", emit: db - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ diamond \\ makedb \\ diff --git a/modules/dragonflye/main.nf b/modules/dragonflye/main.nf index 090c9a13..f9dc9004 100644 --- a/modules/dragonflye/main.nf +++ b/modules/dragonflye/main.nf @@ -27,10 +27,9 @@ process DRAGONFLYE { tuple val(meta), path("{flye,miniasm,raven}.fasta") , emit: raw_contigs tuple val(meta), path("{miniasm,raven}-unpolished.gfa"), optional:true , emit: gfa tuple val(meta), path("flye-info.txt"), optional:true , emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def memory = task.memory.toGiga() """ dragonflye \\ diff --git a/modules/dshbio/exportsegments/main.nf b/modules/dshbio/exportsegments/main.nf index 6016f777..84f59e89 100644 --- a/modules/dshbio/exportsegments/main.nf +++ b/modules/dshbio/exportsegments/main.nf @@ -23,10 +23,9 @@ process DSHBIO_EXPORTSEGMENTS { output: tuple val(meta), path("*.fa"), emit: fasta - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ dsh-bio \\ diff --git a/modules/dshbio/filterbed/main.nf b/modules/dshbio/filterbed/main.nf index 3f2a068d..35039f21 100644 --- a/modules/dshbio/filterbed/main.nf +++ b/modules/dshbio/filterbed/main.nf @@ -23,10 +23,9 @@ process DSHBIO_FILTERBED { output: tuple val(meta), path("*.bed.gz"), emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ dsh-bio \\ diff --git a/modules/dshbio/filtergff3/main.nf b/modules/dshbio/filtergff3/main.nf index 2a1ad816..bf677da8 100644 --- a/modules/dshbio/filtergff3/main.nf +++ b/modules/dshbio/filtergff3/main.nf @@ -23,10 +23,9 @@ process DSHBIO_FILTERGFF3 { output: tuple val(meta), path("*.gff3.gz"), emit: gff3 - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ dsh-bio \\ diff --git a/modules/dshbio/splitbed/main.nf b/modules/dshbio/splitbed/main.nf index 388ba0ef..3e8d656c 100644 --- a/modules/dshbio/splitbed/main.nf +++ b/modules/dshbio/splitbed/main.nf @@ -23,10 +23,9 @@ process DSHBIO_SPLITBED { output: tuple val(meta), path("*.bed.gz"), emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ dsh-bio \\ diff --git a/modules/dshbio/splitgff3/main.nf b/modules/dshbio/splitgff3/main.nf index b8f81392..dd477181 100644 --- a/modules/dshbio/splitgff3/main.nf +++ b/modules/dshbio/splitgff3/main.nf @@ -23,10 +23,9 @@ process DSHBIO_SPLITGFF3 { output: tuple val(meta), path("*.gff3.gz"), emit: gff3 - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ dsh-bio \\ diff --git a/modules/ensemblvep/main.nf b/modules/ensemblvep/main.nf index 17eaf720..ad9c38a6 100644 --- a/modules/ensemblvep/main.nf +++ b/modules/ensemblvep/main.nf @@ -33,10 +33,9 @@ process ENSEMBLVEP { output: tuple val(meta), path("*.ann.vcf"), emit: vcf path "*.summary.html" , emit: report - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" dir_cache = params.use_cache ? "\${PWD}/${cache}" : "/.vep" """ diff --git a/modules/expansionhunter/main.nf b/modules/expansionhunter/main.nf index 1c02f404..845de15d 100644 --- a/modules/expansionhunter/main.nf +++ b/modules/expansionhunter/main.nf @@ -25,10 +25,9 @@ process EXPANSIONHUNTER { output: tuple val(meta), path("*.vcf"), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def gender = (meta.gender == 'male' || meta.gender == 1 || meta.gender == 'XY') ? "male" : "female" """ diff --git a/modules/fastani/main.nf b/modules/fastani/main.nf index 7ee35a0d..5c6366f9 100644 --- a/modules/fastani/main.nf +++ b/modules/fastani/main.nf @@ -24,10 +24,9 @@ process FASTANI { output: tuple val(meta), path("*.ani.txt"), emit: ani - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.batch_input) { diff --git a/modules/fastp/main.nf b/modules/fastp/main.nf index 11cd30b4..e99540d5 100644 --- a/modules/fastp/main.nf +++ b/modules/fastp/main.nf @@ -28,13 +28,12 @@ process FASTP { tuple val(meta), path('*.json') , emit: json tuple val(meta), path('*.html') , emit: html tuple val(meta), path('*.log') , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged script: // Added soft-links to original fastqs for consistent naming in MultiQC - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : '' diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf index 88bfbf5b..9f6cfc55 100644 --- a/modules/fastqc/main.nf +++ b/modules/fastqc/main.nf @@ -24,11 +24,11 @@ process FASTQC { output: tuple val(meta), path("*.html"), emit: html tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: // Add soft-links to original FastQs for consistent naming in pipeline - def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz @@ -36,7 +36,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + ${getSoftwareName(task.process)}: \$( fastqc --version | sed -e "s/FastQC v//g" ) END_VERSIONS """ } else { @@ -47,7 +47,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + ${getSoftwareName(task.process)}: \$( fastqc --version | sed -e "s/FastQC v//g" ) END_VERSIONS """ } diff --git a/modules/fasttree/main.nf b/modules/fasttree/main.nf index 08c093b2..5f81d1f2 100644 --- a/modules/fasttree/main.nf +++ b/modules/fasttree/main.nf @@ -22,10 +22,9 @@ process FASTTREE { output: path "*.tre", emit: phylogeny - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ fasttree \\ $options.args \\ diff --git a/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/fgbio/callmolecularconsensusreads/main.nf index a3d047a7..23056b90 100644 --- a/modules/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/fgbio/callmolecularconsensusreads/main.nf @@ -22,10 +22,9 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ fgbio \\ diff --git a/modules/fgbio/sortbam/main.nf b/modules/fgbio/sortbam/main.nf index 928765f5..34e0b377 100644 --- a/modules/fgbio/sortbam/main.nf +++ b/modules/fgbio/sortbam/main.nf @@ -22,10 +22,9 @@ process FGBIO_SORTBAM { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ fgbio \\ diff --git a/modules/flash/main.nf b/modules/flash/main.nf index f9a381e9..912b2961 100644 --- a/modules/flash/main.nf +++ b/modules/flash/main.nf @@ -22,10 +22,9 @@ process FLASH { output: tuple val(meta), path("*.fastq.gz"), emit: reads - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ flash \\ diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf index 91c23b29..e804bcff 100644 --- a/modules/gatk4/applybqsr/main.nf +++ b/modules/gatk4/applybqsr/main.nf @@ -27,10 +27,9 @@ process GATK4_APPLYBQSR { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def interval = intervals ? "-L ${intervals}" : "" """ diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf index 2f368014..6033fbf1 100644 --- a/modules/gatk4/baserecalibrator/main.nf +++ b/modules/gatk4/baserecalibrator/main.nf @@ -29,10 +29,9 @@ process GATK4_BASERECALIBRATOR { output: tuple val(meta), path("*.table"), emit: table - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : "" def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ') diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf index 28b88f5b..064247cc 100644 --- a/modules/gatk4/bedtointervallist/main.nf +++ b/modules/gatk4/bedtointervallist/main.nf @@ -24,10 +24,9 @@ process GATK4_BEDTOINTERVALLIST { output: tuple val(meta), path('*.interval_list'), emit: interval_list - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ gatk BedToIntervalList \\ diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf index b384d405..12372bdf 100644 --- a/modules/gatk4/createsequencedictionary/main.nf +++ b/modules/gatk4/createsequencedictionary/main.nf @@ -23,10 +23,9 @@ process GATK4_CREATESEQUENCEDICTIONARY { output: path "*.dict" , emit: dict - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def avail_mem = 6 if (!task.memory) { log.info '[GATK] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf index cb8ec0ea..ebd081ac 100644 --- a/modules/gatk4/fastqtosam/main.nf +++ b/modules/gatk4/fastqtosam/main.nf @@ -23,10 +23,9 @@ process GATK4_FASTQTOSAM { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def read_files = meta.single_end ? "-F1 $reads" : "-F1 ${reads[0]} -F2 ${reads[1]}" """ diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf index 782b7653..09449f12 100644 --- a/modules/gatk4/getpileupsummaries/main.nf +++ b/modules/gatk4/getpileupsummaries/main.nf @@ -26,10 +26,9 @@ process GATK4_GETPILEUPSUMMARIES { output: tuple val(meta), path('*.pileups.table'), emit: table - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def sitesCommand = '' diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf index 63771393..01b71ccb 100644 --- a/modules/gatk4/haplotypecaller/main.nf +++ b/modules/gatk4/haplotypecaller/main.nf @@ -27,10 +27,9 @@ process GATK4_HAPLOTYPECALLER { output: tuple val(meta), path("*.vcf.gz"), emit: vcf tuple val(meta), path("*.tbi") , emit: tbi - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def avail_mem = 3 if (!task.memory) { diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf index 99257354..2f464919 100644 --- a/modules/gatk4/intervallisttools/main.nf +++ b/modules/gatk4/intervallisttools/main.nf @@ -23,10 +23,9 @@ process GATK4_INTERVALLISTTOOLS { output: tuple val(meta), path("*_split/*/*.interval_list"), emit: interval_list - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf index 3a3c8e70..8f94f4dd 100644 --- a/modules/gatk4/markduplicates/main.nf +++ b/modules/gatk4/markduplicates/main.nf @@ -24,10 +24,9 @@ process GATK4_MARKDUPLICATES { output: tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.metrics"), emit: metrics - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ gatk MarkDuplicates \\ diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf index 978b7cff..0c9fe5ee 100644 --- a/modules/gatk4/mergebamalignment/main.nf +++ b/modules/gatk4/mergebamalignment/main.nf @@ -26,10 +26,9 @@ process GATK4_MERGEBAMALIGNMENT { output: tuple val(meta), path('*.bam'), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ gatk MergeBamAlignment \\ diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf index c62a6289..ce9a52c3 100644 --- a/modules/gatk4/mergevcfs/main.nf +++ b/modules/gatk4/mergevcfs/main.nf @@ -25,10 +25,9 @@ process GATK4_MERGEVCFS { output: tuple val(meta), path('*.vcf.gz'), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" // Make list of VCFs to merge diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf index c4efc724..9b3f8b3f 100644 --- a/modules/gatk4/mutect2/main.nf +++ b/modules/gatk4/mutect2/main.nf @@ -35,10 +35,9 @@ process GATK4_MUTECT2 { tuple val(meta), path("*.tbi") , emit: tbi tuple val(meta), path("*.stats") , emit: stats tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2 - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def inputsList = [] def normalsList = [] diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf index 0a95b604..b3c9085a 100644 --- a/modules/gatk4/revertsam/main.nf +++ b/modules/gatk4/revertsam/main.nf @@ -23,10 +23,9 @@ process GATK4_REVERTSAM { output: tuple val(meta), path('*.bam'), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ gatk RevertSam \\ diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf index eed7a83f..324f3bae 100644 --- a/modules/gatk4/samtofastq/main.nf +++ b/modules/gatk4/samtofastq/main.nf @@ -23,10 +23,9 @@ process GATK4_SAMTOFASTQ { output: tuple val(meta), path('*.fastq.gz'), emit: fastq - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz" """ diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf index 0c4ba163..793cc671 100644 --- a/modules/gatk4/splitncigarreads/main.nf +++ b/modules/gatk4/splitncigarreads/main.nf @@ -24,10 +24,9 @@ process GATK4_SPLITNCIGARREADS { output: tuple val(meta), path('*.bam'), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ gatk SplitNCigarReads \\ diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf index a79bce8f..28084645 100644 --- a/modules/gatk4/variantfiltration/main.nf +++ b/modules/gatk4/variantfiltration/main.nf @@ -26,11 +26,10 @@ process GATK4_VARIANTFILTRATION { output: tuple val(meta), path("*.vcf"), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ gatk VariantFiltration \\ diff --git a/modules/genmap/index/main.nf b/modules/genmap/index/main.nf index f1168d4e..c79596f0 100644 --- a/modules/genmap/index/main.nf +++ b/modules/genmap/index/main.nf @@ -23,10 +23,9 @@ process GENMAP_INDEX { output: path "genmap" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ genmap \\ index \\ diff --git a/modules/genmap/mappability/main.nf b/modules/genmap/mappability/main.nf index 9eeb4253..4d858cbb 100644 --- a/modules/genmap/mappability/main.nf +++ b/modules/genmap/mappability/main.nf @@ -25,10 +25,9 @@ process GENMAP_MAPPABILITY { path "*.wig" , optional:true, emit: wig path "*.bedgraph" , optional:true, emit: bedgraph path "*.txt" , optional:true, emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ genmap \\ map \\ diff --git a/modules/gffread/main.nf b/modules/gffread/main.nf index 1622e98d..4133ee08 100644 --- a/modules/gffread/main.nf +++ b/modules/gffread/main.nf @@ -23,10 +23,9 @@ process GFFREAD { output: path "*.gtf" , emit: gtf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${gff.baseName}${options.suffix}" : "${gff.baseName}" """ gffread \\ diff --git a/modules/glnexus/main.nf b/modules/glnexus/main.nf index 5cff088b..1384334f 100644 --- a/modules/glnexus/main.nf +++ b/modules/glnexus/main.nf @@ -23,10 +23,9 @@ process GLNEXUS { output: tuple val(meta), path("*.bcf"), emit: bcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" // Make list of GVCFs to merge diff --git a/modules/graphmap2/align/main.nf b/modules/graphmap2/align/main.nf index 30d6cbfd..831b0b3b 100644 --- a/modules/graphmap2/align/main.nf +++ b/modules/graphmap2/align/main.nf @@ -26,10 +26,9 @@ process GRAPHMAP2_ALIGN { output: tuple val(meta), path("*.sam"), emit: sam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ graphmap2 \\ diff --git a/modules/graphmap2/index/main.nf b/modules/graphmap2/index/main.nf index 194c3594..a8b03074 100644 --- a/modules/graphmap2/index/main.nf +++ b/modules/graphmap2/index/main.nf @@ -22,10 +22,9 @@ process GRAPHMAP2_INDEX { output: path "*.gmidx" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ graphmap2 \\ align \\ diff --git a/modules/gubbins/main.nf b/modules/gubbins/main.nf index 10117ae7..da194906 100644 --- a/modules/gubbins/main.nf +++ b/modules/gubbins/main.nf @@ -30,10 +30,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ run_gubbins.py \\ --threads $task.cpus \\ diff --git a/modules/gunzip/main.nf b/modules/gunzip/main.nf index 6a2287b6..aec4569f 100644 --- a/modules/gunzip/main.nf +++ b/modules/gunzip/main.nf @@ -23,10 +23,9 @@ process GUNZIP { output: path "$gunzip", emit: gunzip - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) gunzip = archive.toString() - '.gz' """ gunzip \\ diff --git a/modules/hifiasm/main.nf b/modules/hifiasm/main.nf index 2597afa9..9dfc9618 100644 --- a/modules/hifiasm/main.nf +++ b/modules/hifiasm/main.nf @@ -34,10 +34,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (use_parental_kmers) { """ diff --git a/modules/hisat2/align/main.nf b/modules/hisat2/align/main.nf index 583ddc3f..9b73216b 100644 --- a/modules/hisat2/align/main.nf +++ b/modules/hisat2/align/main.nf @@ -28,12 +28,11 @@ process HISAT2_ALIGN { output: tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.log"), emit: summary - path "versions.yml" , emit: version + path "versions.yml" , emit: versions tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def strandedness = '' diff --git a/modules/hisat2/build/main.nf b/modules/hisat2/build/main.nf index ae24a6aa..015f6f59 100644 --- a/modules/hisat2/build/main.nf +++ b/modules/hisat2/build/main.nf @@ -28,7 +28,7 @@ process HISAT2_BUILD { output: path "hisat2" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: def avail_mem = 0 @@ -53,7 +53,6 @@ process HISAT2_BUILD { log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check." } - def software = getSoftwareName(task.process) """ mkdir hisat2 $extract_exons diff --git a/modules/hisat2/extractsplicesites/main.nf b/modules/hisat2/extractsplicesites/main.nf index 3387cbd1..1c8b7830 100644 --- a/modules/hisat2/extractsplicesites/main.nf +++ b/modules/hisat2/extractsplicesites/main.nf @@ -25,10 +25,9 @@ process HISAT2_EXTRACTSPLICESITES { output: path "*.splice_sites.txt", emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt cat <<-END_VERSIONS > versions.yml diff --git a/modules/hmmer/hmmalign/main.nf b/modules/hmmer/hmmalign/main.nf index a4166fcb..b4292feb 100644 --- a/modules/hmmer/hmmalign/main.nf +++ b/modules/hmmer/hmmalign/main.nf @@ -24,10 +24,9 @@ process HMMER_HMMALIGN { output: tuple val(meta), path("*.sthlm.gz"), emit: sthlm - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def fastacmd = fasta.getExtension() == 'gz' ? "gunzip -c $fasta" : "cat $fasta" """ diff --git a/modules/homer/annotatepeaks/main.nf b/modules/homer/annotatepeaks/main.nf index 198ae1fe..1714644b 100644 --- a/modules/homer/annotatepeaks/main.nf +++ b/modules/homer/annotatepeaks/main.nf @@ -27,10 +27,9 @@ process HOMER_ANNOTATEPEAKS { output: tuple val(meta), path("*annotatePeaks.txt"), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ annotatePeaks.pl \\ diff --git a/modules/homer/findpeaks/main.nf b/modules/homer/findpeaks/main.nf index fe8399a1..2e0b6db9 100644 --- a/modules/homer/findpeaks/main.nf +++ b/modules/homer/findpeaks/main.nf @@ -25,10 +25,9 @@ process HOMER_FINDPEAKS { output: tuple val(meta), path("*peaks.txt"), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ diff --git a/modules/homer/maketagdirectory/main.nf b/modules/homer/maketagdirectory/main.nf index daf0ce60..4f531e82 100644 --- a/modules/homer/maketagdirectory/main.nf +++ b/modules/homer/maketagdirectory/main.nf @@ -26,10 +26,9 @@ process HOMER_MAKETAGDIRECTORY { output: tuple val(meta), path("tag_dir"), emit: tagdir - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ makeTagDirectory \\ diff --git a/modules/homer/makeucscfile/main.nf b/modules/homer/makeucscfile/main.nf index 5b23e243..c56da24b 100644 --- a/modules/homer/makeucscfile/main.nf +++ b/modules/homer/makeucscfile/main.nf @@ -25,10 +25,9 @@ process HOMER_MAKEUCSCFILE { output: tuple val(meta), path("tag_dir/*ucsc.bedGraph.gz"), emit: bedGraph - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ makeUCSCfile \\ diff --git a/modules/iqtree/main.nf b/modules/iqtree/main.nf index 357faf33..bec879df 100644 --- a/modules/iqtree/main.nf +++ b/modules/iqtree/main.nf @@ -24,10 +24,9 @@ process IQTREE { output: path "*.treefile", emit: phylogeny - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def fconst_args = constant_sites ? "-fconst $constant_sites" : '' def memory = task.memory.toString().replaceAll(' ', '') """ diff --git a/modules/ivar/consensus/main.nf b/modules/ivar/consensus/main.nf index b29450b7..33fa11f7 100644 --- a/modules/ivar/consensus/main.nf +++ b/modules/ivar/consensus/main.nf @@ -26,10 +26,9 @@ process IVAR_CONSENSUS { tuple val(meta), path("*.fa") , emit: fasta tuple val(meta), path("*.qual.txt"), emit: qual tuple val(meta), path("*.mpileup") , optional:true, emit: mpileup - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : "" """ diff --git a/modules/ivar/trim/main.nf b/modules/ivar/trim/main.nf index 2a698249..6cf8171c 100644 --- a/modules/ivar/trim/main.nf +++ b/modules/ivar/trim/main.nf @@ -25,10 +25,9 @@ process IVAR_TRIM { output: tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path('*.log'), emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ ivar trim \\ diff --git a/modules/ivar/variants/main.nf b/modules/ivar/variants/main.nf index 2bf82a37..d079a8e9 100644 --- a/modules/ivar/variants/main.nf +++ b/modules/ivar/variants/main.nf @@ -26,10 +26,9 @@ process IVAR_VARIANTS { output: tuple val(meta), path("*.tsv") , emit: tsv tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : "" def features = params.gff ? "-g $gff" : "" diff --git a/modules/kallisto/index/main.nf b/modules/kallisto/index/main.nf index 801f339e..96457b6d 100644 --- a/modules/kallisto/index/main.nf +++ b/modules/kallisto/index/main.nf @@ -23,10 +23,9 @@ process KALLISTO_INDEX { output: path "kallisto" , emit: idx - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ kallisto \\ index \\ diff --git a/modules/kallistobustools/count/main.nf b/modules/kallistobustools/count/main.nf index b0dd3a06..8c705e51 100644 --- a/modules/kallistobustools/count/main.nf +++ b/modules/kallistobustools/count/main.nf @@ -29,10 +29,9 @@ process KALLISTOBUSTOOLS_COUNT { output: tuple val(meta), path ("*.count"), emit: count - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def cdna = t1c ? "-c1 $t1c" : '' def introns = t2c ? "-c2 $t2c" : '' diff --git a/modules/kallistobustools/ref/main.nf b/modules/kallistobustools/ref/main.nf index c8e02687..a8287498 100644 --- a/modules/kallistobustools/ref/main.nf +++ b/modules/kallistobustools/ref/main.nf @@ -24,7 +24,7 @@ process KALLISTOBUSTOOLS_REF { val workflow output: - path "versions.yml" , emit: version + path "versions.yml" , emit: versions path "kb_ref_out.idx" , emit: index path "t2g.txt" , emit: t2g path "cdna.fa" , emit: cdna @@ -33,7 +33,6 @@ process KALLISTOBUSTOOLS_REF { path "intron_t2c.txt" , optional:true, emit: intron_t2c script: - def software = getSoftwareName(task.process) if (workflow == "standard") { """ kb \\ diff --git a/modules/kleborate/main.nf b/modules/kleborate/main.nf index 5a4be104..5bb76ad0 100644 --- a/modules/kleborate/main.nf +++ b/modules/kleborate/main.nf @@ -23,10 +23,9 @@ process KLEBORATE { output: tuple val(meta), path("*.txt"), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ kleborate \\ diff --git a/modules/kraken2/kraken2/main.nf b/modules/kraken2/kraken2/main.nf index cc269e98..0d4e5840 100644 --- a/modules/kraken2/kraken2/main.nf +++ b/modules/kraken2/kraken2/main.nf @@ -26,10 +26,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def paired = meta.single_end ? "" : "--paired" def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq" diff --git a/modules/last/dotplot/main.nf b/modules/last/dotplot/main.nf index ca30bbff..d02e98ad 100644 --- a/modules/last/dotplot/main.nf +++ b/modules/last/dotplot/main.nf @@ -25,10 +25,9 @@ process LAST_DOTPLOT { output: tuple val(meta), path("*.gif"), optional:true, emit: gif tuple val(meta), path("*.png"), optional:true, emit: png - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ last-dotplot \\ diff --git a/modules/last/lastal/main.nf b/modules/last/lastal/main.nf index 3d6518a4..c4335f25 100644 --- a/modules/last/lastal/main.nf +++ b/modules/last/lastal/main.nf @@ -24,10 +24,9 @@ process LAST_LASTAL { output: tuple val(meta), path("*.maf.gz"), emit: maf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def trained_params = param_file ? "-p ${param_file}" : '' """ diff --git a/modules/last/lastdb/main.nf b/modules/last/lastdb/main.nf index ac552e7d..fb765ada 100644 --- a/modules/last/lastdb/main.nf +++ b/modules/last/lastdb/main.nf @@ -23,10 +23,9 @@ process LAST_LASTDB { output: tuple val(meta), path("lastdb"), emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ mkdir lastdb diff --git a/modules/last/mafconvert/main.nf b/modules/last/mafconvert/main.nf index e112cbd8..5e259109 100644 --- a/modules/last/mafconvert/main.nf +++ b/modules/last/mafconvert/main.nf @@ -32,10 +32,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ maf-convert $options.args $format $maf | gzip --no-name \\ diff --git a/modules/last/mafswap/main.nf b/modules/last/mafswap/main.nf index f597693c..5ce38c92 100644 --- a/modules/last/mafswap/main.nf +++ b/modules/last/mafswap/main.nf @@ -23,10 +23,9 @@ process LAST_MAFSWAP { output: tuple val(meta), path("*.maf.gz"), emit: maf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ maf-swap $options.args $maf | gzip --no-name > ${prefix}.swapped.maf.gz diff --git a/modules/last/postmask/main.nf b/modules/last/postmask/main.nf index d3fa02e3..3102fbe6 100644 --- a/modules/last/postmask/main.nf +++ b/modules/last/postmask/main.nf @@ -23,10 +23,9 @@ process LAST_POSTMASK { output: tuple val(meta), path("*.maf.gz"), emit: maf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate" """ diff --git a/modules/last/split/main.nf b/modules/last/split/main.nf index 78d59ed4..2a9e5621 100644 --- a/modules/last/split/main.nf +++ b/modules/last/split/main.nf @@ -23,10 +23,9 @@ process LAST_SPLIT { output: tuple val(meta), path("*.maf.gz"), emit: maf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ zcat < $maf | last-split $options.args | gzip --no-name > ${prefix}.maf.gz diff --git a/modules/last/train/main.nf b/modules/last/train/main.nf index 39728ced..f0b958bc 100644 --- a/modules/last/train/main.nf +++ b/modules/last/train/main.nf @@ -24,10 +24,9 @@ process LAST_TRAIN { output: tuple val(meta), path("*.par"), emit: param_file - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ INDEX_NAME=\$(basename \$(ls $index/*.des) .des) diff --git a/modules/lima/main.nf b/modules/lima/main.nf index 1ff5ac48..16525953 100644 --- a/modules/lima/main.nf +++ b/modules/lima/main.nf @@ -28,7 +28,7 @@ process LIMA { tuple val(meta), path("*.guess") , emit: guess tuple val(meta), path("*.report") , emit: report tuple val(meta), path("*.summary"), emit: summary - path "versions.yml" , emit: version + path "versions.yml" , emit: versions tuple val(meta), path("*.bam") , optional: true, emit: bam tuple val(meta), path("*.bam.pbi") , optional: true, emit: pbi @@ -41,7 +41,6 @@ process LIMA { script: def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" - """ OUT_EXT="" @@ -67,7 +66,7 @@ process LIMA { cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: - lima: \$( lima --version | sed 's/lima //g' | sed 's/ (.\\+//g' ) + ${getSoftwareName(task.process)}: \$( lima --version | sed 's/lima //g' | sed 's/ (.\\+//g' ) END_VERSIONS """ } diff --git a/modules/lofreq/call/main.nf b/modules/lofreq/call/main.nf index 9fb113ff..e77d7a78 100644 --- a/modules/lofreq/call/main.nf +++ b/modules/lofreq/call/main.nf @@ -24,10 +24,9 @@ process LOFREQ_CALL { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ lofreq \\ diff --git a/modules/lofreq/callparallel/main.nf b/modules/lofreq/callparallel/main.nf index 42400793..a86748d7 100644 --- a/modules/lofreq/callparallel/main.nf +++ b/modules/lofreq/callparallel/main.nf @@ -25,10 +25,9 @@ process LOFREQ_CALLPARALLEL { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ lofreq \\ diff --git a/modules/lofreq/filter/main.nf b/modules/lofreq/filter/main.nf index 09c91c8c..905a961d 100644 --- a/modules/lofreq/filter/main.nf +++ b/modules/lofreq/filter/main.nf @@ -23,10 +23,9 @@ process LOFREQ_FILTER { output: tuple val(meta), path("*.gz"), emit: vcf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ lofreq \\ diff --git a/modules/lofreq/indelqual/main.nf b/modules/lofreq/indelqual/main.nf index 78466574..b33a1e04 100644 --- a/modules/lofreq/indelqual/main.nf +++ b/modules/lofreq/indelqual/main.nf @@ -23,10 +23,9 @@ process LOFREQ_INDELQUAL { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ lofreq indelqual \\ diff --git a/modules/macs2/callpeak/main.nf b/modules/macs2/callpeak/main.nf index 4fcd6b05..d54d406d 100644 --- a/modules/macs2/callpeak/main.nf +++ b/modules/macs2/callpeak/main.nf @@ -25,14 +25,13 @@ process MACS2_CALLPEAK { output: tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak tuple val(meta), path("*.xls") , emit: xls - path "versions.yml" , emit: version + path "versions.yml" , emit: versions tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped tuple val(meta), path("*.bed") , optional:true, emit: bed tuple val(meta), path("*.bdg") , optional:true, emit: bdg script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def format = meta.single_end ? 'BAM' : 'BAMPE' def control = controlbam ? "--control $controlbam" : '' diff --git a/modules/malt/build/main.nf b/modules/malt/build/main.nf index 3b494c0c..48259a50 100644 --- a/modules/malt/build/main.nf +++ b/modules/malt/build/main.nf @@ -26,11 +26,10 @@ process MALT_BUILD { output: path "malt_index/" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions path "malt-build.log", emit: log script: - def software = getSoftwareName(task.process) def avail_mem = 6 if (!task.memory) { log.info '[MALT_BUILD] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' diff --git a/modules/malt/run/main.nf b/modules/malt/run/main.nf index 689dabf4..bc78de8c 100644 --- a/modules/malt/run/main.nf +++ b/modules/malt/run/main.nf @@ -27,10 +27,9 @@ process MALT_RUN { path "*.rma6" , emit: rma6 path "*.{tab,text,sam}", optional:true, emit: alignments path "*.log" , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def avail_mem = 6 if (!task.memory) { log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' diff --git a/modules/maltextract/main.nf b/modules/maltextract/main.nf index 426a9fc3..d909ec96 100644 --- a/modules/maltextract/main.nf +++ b/modules/maltextract/main.nf @@ -25,10 +25,9 @@ process MALTEXTRACT { output: path "results" , emit: results - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ MaltExtract \\ -Xmx${task.memory.toGiga()}g \\ diff --git a/modules/mash/sketch/main.nf b/modules/mash/sketch/main.nf index ed018b1a..7a99cc50 100644 --- a/modules/mash/sketch/main.nf +++ b/modules/mash/sketch/main.nf @@ -22,10 +22,9 @@ process MASH_SKETCH { output: tuple val(meta), path("*.msh") , emit: mash tuple val(meta), path("*.mash_stats") , emit: stats - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ mash \\ diff --git a/modules/metaphlan3/main.nf b/modules/metaphlan3/main.nf index 8893c2ab..c5157b66 100644 --- a/modules/metaphlan3/main.nf +++ b/modules/metaphlan3/main.nf @@ -26,10 +26,9 @@ process METAPHLAN3 { tuple val(meta), path("*_profile.txt") , emit: profile tuple val(meta), path("*.biom") , emit: biom tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam" def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input" diff --git a/modules/methyldackel/extract/main.nf b/modules/methyldackel/extract/main.nf index 149f4aa0..94e4b379 100644 --- a/modules/methyldackel/extract/main.nf +++ b/modules/methyldackel/extract/main.nf @@ -25,10 +25,9 @@ process METHYLDACKEL_EXTRACT { output: tuple val(meta), path("*.bedGraph"), emit: bedgraph - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ MethylDackel extract \\ $options.args \\ diff --git a/modules/methyldackel/mbias/main.nf b/modules/methyldackel/mbias/main.nf index 9fa39b82..c8fd2fa2 100644 --- a/modules/methyldackel/mbias/main.nf +++ b/modules/methyldackel/mbias/main.nf @@ -25,10 +25,9 @@ process METHYLDACKEL_MBIAS { output: tuple val(meta), path("*.mbias.txt"), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ MethylDackel mbias \\ diff --git a/modules/minia/main.nf b/modules/minia/main.nf index 9ab344fd..140ef9e7 100644 --- a/modules/minia/main.nf +++ b/modules/minia/main.nf @@ -25,10 +25,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def read_list = reads.join(",") """ diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf index d0ff9c0f..215e4fb5 100644 --- a/modules/minimap2/align/main.nf +++ b/modules/minimap2/align/main.nf @@ -24,10 +24,9 @@ process MINIMAP2_ALIGN { output: tuple val(meta), path("*.paf"), emit: paf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}" """ diff --git a/modules/minimap2/index/main.nf b/modules/minimap2/index/main.nf index cfc40417..b154a649 100644 --- a/modules/minimap2/index/main.nf +++ b/modules/minimap2/index/main.nf @@ -22,10 +22,9 @@ process MINIMAP2_INDEX { output: path "*.mmi" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ minimap2 \\ -t $task.cpus \\ diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index c21ea2a8..8fe3cfee 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -31,10 +31,9 @@ process MOSDEPTH { tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def interval = window_size ? "--by ${window_size}" : "--by ${bed}" """ diff --git a/modules/msisensor/msi/main.nf b/modules/msisensor/msi/main.nf index 41f79b3a..bd5a0a0e 100644 --- a/modules/msisensor/msi/main.nf +++ b/modules/msisensor/msi/main.nf @@ -26,10 +26,9 @@ process MSISENSOR_MSI { tuple val(meta), path("${prefix}_dis") , emit: output_dis tuple val(meta), path("${prefix}_germline"), emit: output_germline tuple val(meta), path("${prefix}_somatic") , emit: output_somatic - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ msisensor \\ diff --git a/modules/msisensor/scan/main.nf b/modules/msisensor/scan/main.nf index 198657ae..ebd8785a 100644 --- a/modules/msisensor/scan/main.nf +++ b/modules/msisensor/scan/main.nf @@ -22,12 +22,11 @@ process MSISENSOR_SCAN { tuple val(meta), path(fasta) output: - tuple (val(meta), path("*.tab"), emit: txt) - path ("versions.yml" , emit: version) + tuple val(meta), path("*.tab"), emit: txt + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) - def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ msisensor \\ scan \\ diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf index 2e7ad932..0861aa59 100644 --- a/modules/multiqc/main.nf +++ b/modules/multiqc/main.nf @@ -24,16 +24,15 @@ process MULTIQC { path "*multiqc_report.html", emit: report path "*_data" , emit: data path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ multiqc -f $options.args . cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + ${getSoftwareName(task.process)}: \$( multiqc --version | sed -e "s/multiqc, version //g" ) END_VERSIONS """ } diff --git a/modules/muscle/main.nf b/modules/muscle/main.nf index ef9bf484..6ffb97ac 100644 --- a/modules/muscle/main.nf +++ b/modules/muscle/main.nf @@ -30,10 +30,9 @@ process MUSCLE { tuple val(meta), path("*.msf") , optional: true, emit: msf tuple val(meta), path("*.tree"), optional: true, emit: tree path "*.log" , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def fasta_out = options.args.contains('-fasta') ? "-fastaout ${prefix}_muscle_msa.afa" : '' def clw_out = options.args.contains('-clw') ? "-clwout ${prefix}_muscle_msa.clw" : '' diff --git a/modules/nanolyse/main.nf b/modules/nanolyse/main.nf index 84cf579a..271592f7 100644 --- a/modules/nanolyse/main.nf +++ b/modules/nanolyse/main.nf @@ -25,10 +25,9 @@ process NANOLYSE { output: tuple val(meta), path("*.fastq.gz"), emit: fastq path "*.log" , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ gunzip -c $fastq | NanoLyse -r $fasta | gzip > ${prefix}.fastq.gz diff --git a/modules/nanoplot/main.nf b/modules/nanoplot/main.nf index e36b2da2..16e2248c 100644 --- a/modules/nanoplot/main.nf +++ b/modules/nanoplot/main.nf @@ -26,10 +26,9 @@ process NANOPLOT { tuple val(meta), path("*.png") , emit: png tuple val(meta), path("*.txt") , emit: txt tuple val(meta), path("*.log") , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" : ("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : '' """ diff --git a/modules/nextclade/main.nf b/modules/nextclade/main.nf index fabf4520..6fc6efc4 100755 --- a/modules/nextclade/main.nf +++ b/modules/nextclade/main.nf @@ -27,10 +27,9 @@ process NEXTCLADE { tuple val(meta), path("${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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ nextclade \\ diff --git a/modules/optitype/main.nf b/modules/optitype/main.nf index 4f136d7c..083b03a7 100644 --- a/modules/optitype/main.nf +++ b/modules/optitype/main.nf @@ -23,10 +23,9 @@ process OPTITYPE { output: tuple val(meta), path("${prefix}"), emit: output - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ diff --git a/modules/pairix/main.nf b/modules/pairix/main.nf index c00af657..4bfd3b0d 100644 --- a/modules/pairix/main.nf +++ b/modules/pairix/main.nf @@ -23,10 +23,9 @@ process PAIRIX { output: tuple val(meta), path(pair), path("*.px2"), emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ pairix \\ $options.args \\ diff --git a/modules/pairtools/dedup/main.nf b/modules/pairtools/dedup/main.nf index 5b901a77..eabf24dd 100644 --- a/modules/pairtools/dedup/main.nf +++ b/modules/pairtools/dedup/main.nf @@ -24,10 +24,9 @@ process PAIRTOOLS_DEDUP { output: tuple val(meta), path("*.pairs.gz") , emit: pairs tuple val(meta), path("*.pairs.stat"), emit: stat - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ pairtools dedup \\ diff --git a/modules/pairtools/flip/main.nf b/modules/pairtools/flip/main.nf index 3010b411..50cfdfd2 100644 --- a/modules/pairtools/flip/main.nf +++ b/modules/pairtools/flip/main.nf @@ -24,10 +24,9 @@ process PAIRTOOLS_FLIP { output: tuple val(meta), path("*.flip.gz"), emit: flip - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ pairtools \\ diff --git a/modules/pairtools/parse/main.nf b/modules/pairtools/parse/main.nf index 66c9257b..cd6099e1 100644 --- a/modules/pairtools/parse/main.nf +++ b/modules/pairtools/parse/main.nf @@ -25,10 +25,9 @@ process PAIRTOOLS_PARSE { output: tuple val(meta), path("*.pairsam.gz") , emit: pairsam tuple val(meta), path("*.pairsam.stat"), emit: stat - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ pairtools \\ diff --git a/modules/pairtools/restrict/main.nf b/modules/pairtools/restrict/main.nf index 31f463ad..b1b21da7 100644 --- a/modules/pairtools/restrict/main.nf +++ b/modules/pairtools/restrict/main.nf @@ -24,10 +24,9 @@ process PAIRTOOLS_RESTRICT { output: tuple val(meta), path("*.pairs.gz"), emit: restrict - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ pairtools \\ diff --git a/modules/pairtools/select/main.nf b/modules/pairtools/select/main.nf index c9218ea9..dec29573 100644 --- a/modules/pairtools/select/main.nf +++ b/modules/pairtools/select/main.nf @@ -24,10 +24,9 @@ process PAIRTOOLS_SELECT { output: tuple val(meta), path("*.selected.pairs.gz") , emit: selected tuple val(meta), path("*.unselected.pairs.gz"), emit: unselected - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ pairtools select \\ diff --git a/modules/pairtools/sort/main.nf b/modules/pairtools/sort/main.nf index 27caed7b..996bcb0b 100644 --- a/modules/pairtools/sort/main.nf +++ b/modules/pairtools/sort/main.nf @@ -23,10 +23,9 @@ process PAIRTOOLS_SORT { output: tuple val(meta), path("*.pairs.gz"), emit: sorted - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def mem = task.memory.toString().replaceAll(/(\s|\.|B)+/, '') """ diff --git a/modules/pangolin/main.nf b/modules/pangolin/main.nf index 5292d1c3..edf67dd7 100644 --- a/modules/pangolin/main.nf +++ b/modules/pangolin/main.nf @@ -23,10 +23,9 @@ process PANGOLIN { output: tuple val(meta), path('*.csv'), emit: report - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ pangolin \\ diff --git a/modules/pbccs/main.nf b/modules/pbccs/main.nf index 5df852cf..49c47fda 100644 --- a/modules/pbccs/main.nf +++ b/modules/pbccs/main.nf @@ -29,11 +29,9 @@ 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("versions.yml" ) , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) - // def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def ccs = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs.bam' def report_txt = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.txt' def report_json = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.json' diff --git a/modules/phantompeakqualtools/main.nf b/modules/phantompeakqualtools/main.nf index 166ed8be..b390bf7e 100644 --- a/modules/phantompeakqualtools/main.nf +++ b/modules/phantompeakqualtools/main.nf @@ -27,10 +27,9 @@ process PHANTOMPEAKQUALTOOLS { tuple val(meta), path("*.out") , emit: spp tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.Rdata"), emit: rdata - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ RUN_SPP=`which run_spp.R` diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf index 11ddee9b..dd8fdaca 100644 --- a/modules/picard/collectmultiplemetrics/main.nf +++ b/modules/picard/collectmultiplemetrics/main.nf @@ -25,10 +25,9 @@ process PICARD_COLLECTMULTIPLEMETRICS { output: tuple val(meta), path("*_metrics"), emit: metrics tuple val(meta), path("*.pdf") , emit: pdf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def avail_mem = 3 if (!task.memory) { diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf index b5d11839..6028feef 100644 --- a/modules/picard/collectwgsmetrics/main.nf +++ b/modules/picard/collectwgsmetrics/main.nf @@ -24,10 +24,9 @@ process PICARD_COLLECTWGSMETRICS { output: tuple val(meta), path("*_metrics"), emit: metrics - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def avail_mem = 3 if (!task.memory) { diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf index c7e40d27..68cee34d 100644 --- a/modules/picard/filtersamreads/main.nf +++ b/modules/picard/filtersamreads/main.nf @@ -24,10 +24,9 @@ process PICARD_FILTERSAMREADS { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def avail_mem = 3 if (!task.memory) { diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf index dc8d460b..37b825d7 100644 --- a/modules/picard/markduplicates/main.nf +++ b/modules/picard/markduplicates/main.nf @@ -25,10 +25,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def avail_mem = 3 if (!task.memory) { diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf index c6ecfe58..355c0bf3 100644 --- a/modules/picard/mergesamfiles/main.nf +++ b/modules/picard/mergesamfiles/main.nf @@ -23,10 +23,9 @@ process PICARD_MERGESAMFILES { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def bam_files = bams.sort() def avail_mem = 3 diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf index 475a30f9..939df1c0 100644 --- a/modules/picard/sortsam/main.nf +++ b/modules/picard/sortsam/main.nf @@ -25,10 +25,9 @@ process PICARD_SORTSAM { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def avail_mem = 3 if (!task.memory) { diff --git a/modules/plasmidid/main.nf b/modules/plasmidid/main.nf index 792b3c12..1edc5eeb 100644 --- a/modules/plasmidid/main.nf +++ b/modules/plasmidid/main.nf @@ -31,10 +31,9 @@ process PLASMIDID { tuple val(meta), path("${prefix}/database/") , emit: database tuple val(meta), path("${prefix}/fasta_files/") , emit: fasta_files tuple val(meta), path("${prefix}/kmer/") , emit: kmer - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ plasmidID \\ diff --git a/modules/plink/vcf/main.nf b/modules/plink/vcf/main.nf index 735fef88..a676b723 100644 --- a/modules/plink/vcf/main.nf +++ b/modules/plink/vcf/main.nf @@ -26,10 +26,9 @@ process PLINK_VCF { tuple val(meta), path("*.bim"), emit: bim, optional: true tuple val(meta), path("*.fam"), emit: fam, optional: true - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ @@ -41,7 +40,7 @@ process PLINK_VCF { cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: - plink: \$(echo \$(plink --version 2>&1) | sed 's/^PLINK v//' | sed 's/..-bit.*//' ) + ${getSoftwareName(task.process)}: \$(echo \$(plink --version 2>&1) | sed 's/^PLINK v//' | sed 's/..-bit.*//' ) END_VERSIONS """ } diff --git a/modules/preseq/lcextrap/main.nf b/modules/preseq/lcextrap/main.nf index 69f682d3..f551a549 100644 --- a/modules/preseq/lcextrap/main.nf +++ b/modules/preseq/lcextrap/main.nf @@ -25,10 +25,9 @@ process PRESEQ_LCEXTRAP { output: tuple val(meta), path("*.ccurve.txt"), emit: ccurve tuple val(meta), path("*.log") , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def paired_end = meta.single_end ? '' : '-pe' """ diff --git a/modules/prodigal/main.nf b/modules/prodigal/main.nf index 6944f86b..572ffe92 100644 --- a/modules/prodigal/main.nf +++ b/modules/prodigal/main.nf @@ -27,10 +27,9 @@ 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("${prefix}_all.txt"), emit: all_gene_annotations - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ prodigal -i "${genome}" \\ diff --git a/modules/prokka/main.nf b/modules/prokka/main.nf index 8aefda7c..fb86078c 100644 --- a/modules/prokka/main.nf +++ b/modules/prokka/main.nf @@ -35,10 +35,9 @@ process PROKKA { tuple val(meta), path("${prefix}/*.log"), emit: log tuple val(meta), path("${prefix}/*.txt"), emit: txt tuple val(meta), path("${prefix}/*.tsv"), emit: tsv - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def proteins_opt = proteins ? "--proteins ${proteins[0]}" : "" def prodigal_opt = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : "" diff --git a/modules/pycoqc/main.nf b/modules/pycoqc/main.nf index f3b164ee..2c263d61 100644 --- a/modules/pycoqc/main.nf +++ b/modules/pycoqc/main.nf @@ -24,10 +24,9 @@ process PYCOQC { output: path "*.html" , emit: html path "*.json" , emit: json - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ pycoQC \\ $options.args \\ diff --git a/modules/pydamage/analyze/main.nf b/modules/pydamage/analyze/main.nf index df787e44..9cfb8a1a 100644 --- a/modules/pydamage/analyze/main.nf +++ b/modules/pydamage/analyze/main.nf @@ -23,10 +23,9 @@ process PYDAMAGE_ANALYZE { output: tuple val(meta), path("pydamage_results/pydamage_results.csv"), emit: csv - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ pydamage \\ diff --git a/modules/pydamage/filter/main.nf b/modules/pydamage/filter/main.nf index 87677367..6cd7ae7a 100644 --- a/modules/pydamage/filter/main.nf +++ b/modules/pydamage/filter/main.nf @@ -23,10 +23,9 @@ process PYDAMAGE_FILTER { output: tuple val(meta), path("pydamage_results/pydamage_filtered_results.csv"), emit: csv - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ diff --git a/modules/qcat/main.nf b/modules/qcat/main.nf index be239816..b650fb8c 100644 --- a/modules/qcat/main.nf +++ b/modules/qcat/main.nf @@ -24,10 +24,9 @@ process QCAT { output: tuple val(meta), path("fastq/*.fastq.gz"), emit: reads - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ ## Unzip fastq file diff --git a/modules/qualimap/bamqc/main.nf b/modules/qualimap/bamqc/main.nf index 0cc101ef..d33f1e67 100644 --- a/modules/qualimap/bamqc/main.nf +++ b/modules/qualimap/bamqc/main.nf @@ -25,10 +25,9 @@ process QUALIMAP_BAMQC { output: tuple val(meta), path("${prefix}"), emit: results - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs' diff --git a/modules/qualimap/rnaseq/main.nf b/modules/qualimap/rnaseq/main.nf index fa32a6a7..9492cec6 100644 --- a/modules/qualimap/rnaseq/main.nf +++ b/modules/qualimap/rnaseq/main.nf @@ -24,10 +24,9 @@ process QUALIMAP_RNASEQ { output: tuple val(meta), path("${prefix}"), emit: results - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def paired_end = meta.single_end ? '' : '-pe' def memory = task.memory.toGiga() + "G" diff --git a/modules/quast/main.nf b/modules/quast/main.nf index 97ff93e2..072d649d 100644 --- a/modules/quast/main.nf +++ b/modules/quast/main.nf @@ -27,10 +27,9 @@ process QUAST { output: path "${prefix}" , emit: results path '*.tsv' , emit: tsv - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ?: software def features = use_gff ? "--features $gff" : '' def reference = use_fasta ? "-r $fasta" : '' diff --git a/modules/rapidnj/main.nf b/modules/rapidnj/main.nf index 118ea7af..aa23b56e 100644 --- a/modules/rapidnj/main.nf +++ b/modules/rapidnj/main.nf @@ -25,10 +25,9 @@ process RAPIDNJ { output: path "*.sth" , emit: stockholm_alignment path "*.tre" , emit: phylogeny - path "versions.yml", emit: version + path "versions.yml", emit: versions script: - def software = getSoftwareName(task.process) """ python \\ -c 'from Bio import SeqIO; SeqIO.convert("$alignment", "fasta", "alignment.sth", "stockholm")' diff --git a/modules/rasusa/main.nf b/modules/rasusa/main.nf index 88f3a208..b9ba0b13 100644 --- a/modules/rasusa/main.nf +++ b/modules/rasusa/main.nf @@ -24,10 +24,9 @@ process RASUSA { output: tuple val(meta), path('*.fastq.gz'), emit: reads - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def output = meta.single_end ? "--output ${prefix}.fastq.gz" : "--output ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz" """ diff --git a/modules/raxmlng/main.nf b/modules/raxmlng/main.nf index e3bde2f3..f607b506 100644 --- a/modules/raxmlng/main.nf +++ b/modules/raxmlng/main.nf @@ -23,10 +23,9 @@ process RAXMLNG { output: path "*.raxml.bestTree", emit: phylogeny path "*.raxml.support" , optional:true, emit: phylogeny_bootstrapped - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ raxml-ng \\ $options.args \\ diff --git a/modules/rsem/calculateexpression/main.nf b/modules/rsem/calculateexpression/main.nf index d3d11397..f19392f7 100644 --- a/modules/rsem/calculateexpression/main.nf +++ b/modules/rsem/calculateexpression/main.nf @@ -27,14 +27,13 @@ process RSEM_CALCULATEEXPRESSION { tuple val(meta), path("*.isoforms.results"), emit: counts_transcript tuple val(meta), path("*.stat") , emit: stat tuple val(meta), path("*.log") , emit: logs - path "versions.yml" , emit: version + path "versions.yml" , emit: versions tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star tuple val(meta), path("${prefix}.genome.bam") , optional:true, emit: bam_genome tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def strandedness = '' diff --git a/modules/rsem/preparereference/main.nf b/modules/rsem/preparereference/main.nf index b4a613bd..7e671207 100644 --- a/modules/rsem/preparereference/main.nf +++ b/modules/rsem/preparereference/main.nf @@ -25,10 +25,9 @@ process RSEM_PREPAREREFERENCE { output: path "rsem" , emit: index path "rsem/*transcripts.fa", emit: transcript_fasta - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def args = options.args.tokenize() if (args.contains('--star')) { args.removeIf { it.contains('--star') } diff --git a/modules/rseqc/bamstat/main.nf b/modules/rseqc/bamstat/main.nf index fa71dd11..64939add 100644 --- a/modules/rseqc/bamstat/main.nf +++ b/modules/rseqc/bamstat/main.nf @@ -23,10 +23,9 @@ process RSEQC_BAMSTAT { output: tuple val(meta), path("*.bam_stat.txt"), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bam_stat.py \\ diff --git a/modules/rseqc/inferexperiment/main.nf b/modules/rseqc/inferexperiment/main.nf index a9842c0d..c5e94943 100644 --- a/modules/rseqc/inferexperiment/main.nf +++ b/modules/rseqc/inferexperiment/main.nf @@ -24,10 +24,9 @@ process RSEQC_INFEREXPERIMENT { output: tuple val(meta), path("*.infer_experiment.txt"), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ infer_experiment.py \\ diff --git a/modules/rseqc/innerdistance/main.nf b/modules/rseqc/innerdistance/main.nf index d98780f1..622cd5cd 100644 --- a/modules/rseqc/innerdistance/main.nf +++ b/modules/rseqc/innerdistance/main.nf @@ -28,10 +28,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (!meta.single_end) { """ diff --git a/modules/rseqc/junctionannotation/main.nf b/modules/rseqc/junctionannotation/main.nf index cfb12d69..1b75d915 100644 --- a/modules/rseqc/junctionannotation/main.nf +++ b/modules/rseqc/junctionannotation/main.nf @@ -30,10 +30,9 @@ process RSEQC_JUNCTIONANNOTATION { tuple val(meta), path("*.Interact.bed"), optional:true, emit: interact_bed tuple val(meta), path("*junction.pdf") , optional:true, emit: pdf tuple val(meta), path("*events.pdf") , optional:true, emit: events_pdf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ junction_annotation.py \\ diff --git a/modules/rseqc/junctionsaturation/main.nf b/modules/rseqc/junctionsaturation/main.nf index a5aa5461..fa435aea 100644 --- a/modules/rseqc/junctionsaturation/main.nf +++ b/modules/rseqc/junctionsaturation/main.nf @@ -25,10 +25,9 @@ process RSEQC_JUNCTIONSATURATION { output: tuple val(meta), path("*.pdf"), emit: pdf tuple val(meta), path("*.r") , emit: rscript - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ junction_saturation.py \\ diff --git a/modules/rseqc/readdistribution/main.nf b/modules/rseqc/readdistribution/main.nf index 56086c89..0c83fdf0 100644 --- a/modules/rseqc/readdistribution/main.nf +++ b/modules/rseqc/readdistribution/main.nf @@ -24,10 +24,9 @@ process RSEQC_READDISTRIBUTION { output: tuple val(meta), path("*.read_distribution.txt"), emit: txt - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ read_distribution.py \\ diff --git a/modules/rseqc/readduplication/main.nf b/modules/rseqc/readduplication/main.nf index ca7c2b13..bee82682 100644 --- a/modules/rseqc/readduplication/main.nf +++ b/modules/rseqc/readduplication/main.nf @@ -26,10 +26,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ read_duplication.py \\ diff --git a/modules/salmon/index/main.nf b/modules/salmon/index/main.nf index 9e62eb8a..c3fcef01 100644 --- a/modules/salmon/index/main.nf +++ b/modules/salmon/index/main.nf @@ -24,10 +24,9 @@ process SALMON_INDEX { output: path "salmon" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt" def gentrome = "gentrome.fa" if (genome_fasta.endsWith('.gz')) { diff --git a/modules/salmon/quant/main.nf b/modules/salmon/quant/main.nf index 397bdd31..7c2e0e17 100644 --- a/modules/salmon/quant/main.nf +++ b/modules/salmon/quant/main.nf @@ -28,10 +28,9 @@ process SALMON_QUANT { output: tuple val(meta), path("${prefix}"), emit: results - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def reference = "--index $index" diff --git a/modules/samtools/ampliconclip/main.nf b/modules/samtools/ampliconclip/main.nf index cccf2f7c..3da1d6fe 100644 --- a/modules/samtools/ampliconclip/main.nf +++ b/modules/samtools/ampliconclip/main.nf @@ -28,10 +28,9 @@ process SAMTOOLS_AMPLICONCLIP { tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.clipstats.txt") , optional:true, emit: stats tuple val(meta), path("*.cliprejects.bam"), optional:true, emit: rejects_bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : "" def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : "" diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf index cdbae99b..80cedeab 100644 --- a/modules/samtools/faidx/main.nf +++ b/modules/samtools/faidx/main.nf @@ -23,10 +23,9 @@ process SAMTOOLS_FAIDX { output: path "*.fai" , emit: fai - path "versions.yml", emit: version + path "versions.yml", emit: versions script: - def software = getSoftwareName(task.process) """ samtools faidx $fasta cat <<-END_VERSIONS > versions.yml diff --git a/modules/samtools/fastq/main.nf b/modules/samtools/fastq/main.nf index 02110870..0b454360 100644 --- a/modules/samtools/fastq/main.nf +++ b/modules/samtools/fastq/main.nf @@ -23,10 +23,9 @@ process SAMTOOLS_FASTQ { output: tuple val(meta), path("*.fastq.gz"), emit: fastq - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz" diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf index d0cf86aa..f9115c6b 100644 --- a/modules/samtools/flagstat/main.nf +++ b/modules/samtools/flagstat/main.nf @@ -23,10 +23,9 @@ process SAMTOOLS_FLAGSTAT { output: tuple val(meta), path("*.flagstat"), emit: flagstat - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ samtools flagstat $bam > ${bam}.flagstat cat <<-END_VERSIONS > versions.yml diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf index 06a07964..b005088a 100644 --- a/modules/samtools/idxstats/main.nf +++ b/modules/samtools/idxstats/main.nf @@ -23,10 +23,9 @@ process SAMTOOLS_IDXSTATS { output: tuple val(meta), path("*.idxstats"), emit: idxstats - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ samtools idxstats $bam > ${bam}.idxstats cat <<-END_VERSIONS > versions.yml diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf index c2ba4de7..febbc11c 100644 --- a/modules/samtools/index/main.nf +++ b/modules/samtools/index/main.nf @@ -24,10 +24,9 @@ process SAMTOOLS_INDEX { output: tuple val(meta), path("*.bai"), optional:true, emit: bai tuple val(meta), path("*.csi"), optional:true, emit: csi - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ samtools index $options.args $bam cat <<-END_VERSIONS > versions.yml diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf index ec574105..34c40d57 100644 --- a/modules/samtools/merge/main.nf +++ b/modules/samtools/merge/main.nf @@ -23,10 +23,9 @@ process SAMTOOLS_MERGE { output: tuple val(meta), path("${prefix}.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ samtools merge ${prefix}.bam $bams diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf index 903bfd33..9e120526 100644 --- a/modules/samtools/mpileup/main.nf +++ b/modules/samtools/mpileup/main.nf @@ -24,10 +24,9 @@ process SAMTOOLS_MPILEUP { output: tuple val(meta), path("*.mpileup"), emit: mpileup - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ samtools mpileup \\ diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf index edd558bf..b30f6f45 100644 --- a/modules/samtools/sort/main.nf +++ b/modules/samtools/sort/main.nf @@ -23,10 +23,9 @@ process SAMTOOLS_SORT { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions 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 diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf index 823b5f31..6218dd2d 100644 --- a/modules/samtools/stats/main.nf +++ b/modules/samtools/stats/main.nf @@ -23,10 +23,9 @@ process SAMTOOLS_STATS { output: tuple val(meta), path("*.stats"), emit: stats - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ samtools stats $bam > ${bam}.stats cat <<-END_VERSIONS > versions.yml diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf index 110d5abf..ec1663e0 100644 --- a/modules/samtools/view/main.nf +++ b/modules/samtools/view/main.nf @@ -23,10 +23,9 @@ process SAMTOOLS_VIEW { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ samtools view $options.args $bam > ${prefix}.bam diff --git a/modules/seacr/callpeak/main.nf b/modules/seacr/callpeak/main.nf index 8892ab6d..4c3fd922 100644 --- a/modules/seacr/callpeak/main.nf +++ b/modules/seacr/callpeak/main.nf @@ -25,10 +25,9 @@ process SEACR_CALLPEAK { output: tuple val(meta), path("*.bed"), emit: bed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ SEACR_1.3.sh \\ diff --git a/modules/seqkit/split2/main.nf b/modules/seqkit/split2/main.nf index b178b1da..80f55bb6 100644 --- a/modules/seqkit/split2/main.nf +++ b/modules/seqkit/split2/main.nf @@ -23,10 +23,9 @@ process SEQKIT_SPLIT2 { output: tuple val(meta), path("*${prefix}/*.gz"), emit: reads - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if(meta.single_end){ """ diff --git a/modules/seqtk/sample/main.nf b/modules/seqtk/sample/main.nf index 277d74ca..3b039fb9 100644 --- a/modules/seqtk/sample/main.nf +++ b/modules/seqtk/sample/main.nf @@ -24,10 +24,9 @@ process SEQTK_SAMPLE { output: tuple val(meta), path("*.fastq.gz"), emit: reads - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { """ diff --git a/modules/seqtk/subseq/main.nf b/modules/seqtk/subseq/main.nf index 41326402..df8783de 100644 --- a/modules/seqtk/subseq/main.nf +++ b/modules/seqtk/subseq/main.nf @@ -24,10 +24,9 @@ process SEQTK_SUBSEQ { output: path "*.gz" , emit: sequences - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ?: '' def ext = "fa" if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) { diff --git a/modules/sequenzautils/bam2seqz/main.nf b/modules/sequenzautils/bam2seqz/main.nf index 9c4fc12f..61ca70c6 100644 --- a/modules/sequenzautils/bam2seqz/main.nf +++ b/modules/sequenzautils/bam2seqz/main.nf @@ -25,10 +25,9 @@ process SEQUENZAUTILS_BAM2SEQZ { output: tuple val(meta), path("*.gz"), emit: seqz - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ sequenza-utils \\ diff --git a/modules/sequenzautils/gcwiggle/main.nf b/modules/sequenzautils/gcwiggle/main.nf index a352256a..c952bb70 100644 --- a/modules/sequenzautils/gcwiggle/main.nf +++ b/modules/sequenzautils/gcwiggle/main.nf @@ -23,10 +23,9 @@ process SEQUENZAUTILS_GCWIGGLE { output: tuple val(meta), path("*.wig.gz"), emit: wig - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ sequenza-utils \\ diff --git a/modules/seqwish/induce/main.nf b/modules/seqwish/induce/main.nf index e9b2836b..aaabce51 100644 --- a/modules/seqwish/induce/main.nf +++ b/modules/seqwish/induce/main.nf @@ -25,11 +25,10 @@ process SEQWISH_INDUCE { output: tuple val(meta), path("*.gfa"), emit: gfa - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ seqwish \\ diff --git a/modules/shovill/main.nf b/modules/shovill/main.nf index 92b10732..48425f9f 100644 --- a/modules/shovill/main.nf +++ b/modules/shovill/main.nf @@ -27,10 +27,9 @@ process SHOVILL { tuple val(meta), path("shovill.log") , emit: log tuple val(meta), path("{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs tuple val(meta), path("contigs.{fastg,gfa,LastGraph}") , optional:true, emit: gfa - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def memory = task.memory.toGiga() """ shovill \\ diff --git a/modules/snpdists/main.nf b/modules/snpdists/main.nf index ede94906..506a922a 100644 --- a/modules/snpdists/main.nf +++ b/modules/snpdists/main.nf @@ -23,10 +23,9 @@ process SNPDISTS { output: tuple val(meta), path("*.tsv"), emit: tsv - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ snp-dists \\ diff --git a/modules/snpeff/main.nf b/modules/snpeff/main.nf index 8b30360a..3a1f6a52 100644 --- a/modules/snpeff/main.nf +++ b/modules/snpeff/main.nf @@ -31,10 +31,9 @@ process SNPEFF { output: tuple val(meta), path("*.ann.vcf"), emit: vcf path "*.csv" , emit: report - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def avail_mem = 6 if (!task.memory) { log.info '[snpEff] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' diff --git a/modules/snpsites/main.nf b/modules/snpsites/main.nf index 5cc85773..543ee01c 100644 --- a/modules/snpsites/main.nf +++ b/modules/snpsites/main.nf @@ -23,11 +23,10 @@ process SNPSITES { output: path "*.fas" , emit: fasta path "*.sites.txt" , emit: constant_sites - path "versions.yml" , emit: version + path "versions.yml" , emit: versions env CONSTANT_SITES, emit: constant_sites_string script: - def software = getSoftwareName(task.process) """ snp-sites \\ $alignment \\ diff --git a/modules/sortmerna/main.nf b/modules/sortmerna/main.nf index 01975979..f35b1468 100644 --- a/modules/sortmerna/main.nf +++ b/modules/sortmerna/main.nf @@ -25,10 +25,9 @@ process SORTMERNA { output: tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), path("*.log") , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def Refs = "" diff --git a/modules/spades/main.nf b/modules/spades/main.nf index a260de54..c21066e2 100644 --- a/modules/spades/main.nf +++ b/modules/spades/main.nf @@ -29,10 +29,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}" def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : "" diff --git a/modules/staphopiasccmec/main.nf b/modules/staphopiasccmec/main.nf index 0e57128b..08def401 100644 --- a/modules/staphopiasccmec/main.nf +++ b/modules/staphopiasccmec/main.nf @@ -23,10 +23,9 @@ process STAPHOPIASCCMEC { output: tuple val(meta), path("*.tsv"), emit: tsv - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ staphopia-sccmec --assembly $fasta $options.args > ${prefix}.tsv diff --git a/modules/star/align/main.nf b/modules/star/align/main.nf index 677d1f2a..e0ccba8c 100644 --- a/modules/star/align/main.nf +++ b/modules/star/align/main.nf @@ -29,7 +29,7 @@ process STAR_ALIGN { tuple val(meta), path('*Log.final.out') , emit: log_final tuple val(meta), path('*Log.out') , emit: log_out tuple val(meta), path('*Log.progress.out'), emit: log_progress - path "versions.yml" , emit: version + path "versions.yml" , emit: versions tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript @@ -39,7 +39,6 @@ process STAR_ALIGN { tuple val(meta), path('*.out.junction') , optional:true, emit: junction script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf" def seq_platform = params.seq_platform ? "'PL:$params.seq_platform'" : "" diff --git a/modules/star/genomegenerate/main.nf b/modules/star/genomegenerate/main.nf index 520f6b21..c932fafe 100644 --- a/modules/star/genomegenerate/main.nf +++ b/modules/star/genomegenerate/main.nf @@ -25,10 +25,9 @@ process STAR_GENOMEGENERATE { output: path "star" , emit: index - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' def args = options.args.tokenize() if (args.contains('--genomeSAindexNbases')) { diff --git a/modules/strelka/germline/main.nf b/modules/strelka/germline/main.nf index d2203fa4..64a01e6c 100644 --- a/modules/strelka/germline/main.nf +++ b/modules/strelka/germline/main.nf @@ -29,10 +29,9 @@ process STRELKA_GERMLINE { tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi tuple val(meta), path("*genome.vcf.gz") , emit: genome_vcf tuple val(meta), path("*genome.vcf.gz.tbi") , emit: genome_vcf_tbi - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def regions = params.target_bed ? "--exome --callRegions ${target_bed}" : "" """ @@ -51,7 +50,7 @@ process STRELKA_GERMLINE { cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: - strelka: \$( configureStrelkaGermlineWorkflow.py --version ) + ${getSoftwareName(task.process)}: \$( configureStrelkaGermlineWorkflow.py --version ) END_VERSIONS """ } diff --git a/modules/stringtie/merge/main.nf b/modules/stringtie/merge/main.nf index 85670a91..371533bb 100644 --- a/modules/stringtie/merge/main.nf +++ b/modules/stringtie/merge/main.nf @@ -24,10 +24,9 @@ process STRINGTIE_MERGE { output: path "stringtie.merged.gtf", emit: gtf - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ stringtie \\ --merge $stringtie_gtf \\ diff --git a/modules/stringtie/stringtie/main.nf b/modules/stringtie/stringtie/main.nf index 92986dba..3579e47c 100644 --- a/modules/stringtie/stringtie/main.nf +++ b/modules/stringtie/stringtie/main.nf @@ -27,10 +27,9 @@ process STRINGTIE { tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf tuple val(meta), path("*.abundance.txt") , emit: abundance tuple val(meta), path("*.ballgown") , emit: ballgown - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def strandedness = '' diff --git a/modules/subread/featurecounts/main.nf b/modules/subread/featurecounts/main.nf index 76209a0d..0a0285db 100644 --- a/modules/subread/featurecounts/main.nf +++ b/modules/subread/featurecounts/main.nf @@ -24,10 +24,9 @@ process SUBREAD_FEATURECOUNTS { output: tuple val(meta), path("*featureCounts.txt") , emit: counts tuple val(meta), path("*featureCounts.txt.summary"), emit: summary - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def paired_end = meta.single_end ? '' : '-p' diff --git a/modules/tabix/bgzip/main.nf b/modules/tabix/bgzip/main.nf index c76588df..43726f17 100644 --- a/modules/tabix/bgzip/main.nf +++ b/modules/tabix/bgzip/main.nf @@ -23,10 +23,9 @@ process TABIX_BGZIP { output: tuple val(meta), path("*.gz"), emit: gz - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bgzip -c $options.args $input > ${prefix}.${input.getExtension()}.gz diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf index 302c8500..e44a7226 100644 --- a/modules/tabix/bgziptabix/main.nf +++ b/modules/tabix/bgziptabix/main.nf @@ -23,10 +23,9 @@ process TABIX_BGZIPTABIX { output: tuple val(meta), path("*.gz"), path("*.tbi"), emit: tbi - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bgzip -c $options.args $input > ${prefix}.gz diff --git a/modules/tabix/tabix/main.nf b/modules/tabix/tabix/main.nf index 1fabeba4..1574c0b5 100644 --- a/modules/tabix/tabix/main.nf +++ b/modules/tabix/tabix/main.nf @@ -23,10 +23,9 @@ process TABIX_TABIX { output: tuple val(meta), path("*.tbi"), emit: tbi - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ tabix $options.args $tab diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf index fce5c49b..e262221a 100644 --- a/modules/tiddit/sv/main.nf +++ b/modules/tiddit/sv/main.nf @@ -27,10 +27,9 @@ process TIDDIT_SV { tuple val(meta), path("*.vcf") , emit: vcf tuple val(meta), path("*.ploidy.tab") , emit: ploidy tuple val(meta), path("*.signals.tab"), emit: signals - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : "" """ diff --git a/modules/trimgalore/main.nf b/modules/trimgalore/main.nf index 6f5a65c2..8e77f1f7 100644 --- a/modules/trimgalore/main.nf +++ b/modules/trimgalore/main.nf @@ -24,7 +24,7 @@ process TRIMGALORE { output: tuple val(meta), path("*.fq.gz") , emit: reads tuple val(meta), path("*report.txt"), emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions tuple val(meta), path("*.html"), emit: html optional true tuple val(meta), path("*.zip") , emit: zip optional true @@ -48,7 +48,6 @@ process TRIMGALORE { def tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : '' // Added soft-links to original fastqs for consistent naming in MultiQC - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { """ diff --git a/modules/ucsc/bed12tobigbed/main.nf b/modules/ucsc/bed12tobigbed/main.nf index 2f9b287b..81f39a6f 100644 --- a/modules/ucsc/bed12tobigbed/main.nf +++ b/modules/ucsc/bed12tobigbed/main.nf @@ -26,10 +26,9 @@ process UCSC_BED12TOBIGBED { output: tuple val(meta), path("*.bigBed"), emit: bigbed - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedToBigBed \\ diff --git a/modules/ucsc/bedclip/main.nf b/modules/ucsc/bedclip/main.nf index c001b410..5fbc2b3b 100755 --- a/modules/ucsc/bedclip/main.nf +++ b/modules/ucsc/bedclip/main.nf @@ -26,10 +26,9 @@ process UCSC_BEDCLIP { output: tuple val(meta), path("*.bedGraph"), emit: bedgraph - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedClip \\ diff --git a/modules/ucsc/bedgraphtobigwig/main.nf b/modules/ucsc/bedgraphtobigwig/main.nf index 4a779644..f55cdb07 100644 --- a/modules/ucsc/bedgraphtobigwig/main.nf +++ b/modules/ucsc/bedgraphtobigwig/main.nf @@ -26,10 +26,9 @@ process UCSC_BEDGRAPHTOBIGWIG { output: tuple val(meta), path("*.bigWig"), emit: bigwig - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedGraphToBigWig \\ diff --git a/modules/ucsc/bigwigaverageoverbed/main.nf b/modules/ucsc/bigwigaverageoverbed/main.nf index 76c00cfe..72491443 100644 --- a/modules/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/ucsc/bigwigaverageoverbed/main.nf @@ -26,10 +26,9 @@ process UCSC_BIGWIGAVERAGEOVERBED { output: tuple val(meta), path("*.tab"), emit: tab - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ # there is a bug that bigWigAverageOverBed can not handle ensembl seqlevels style. diff --git a/modules/ucsc/wigtobigwig/main.nf b/modules/ucsc/wigtobigwig/main.nf index 29e5cd99..d03a2c4a 100644 --- a/modules/ucsc/wigtobigwig/main.nf +++ b/modules/ucsc/wigtobigwig/main.nf @@ -26,10 +26,9 @@ process UCSC_WIGTOBIGWIG { output: path "*.bw" , emit: bw - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) """ wigToBigWig \\ diff --git a/modules/umitools/dedup/main.nf b/modules/umitools/dedup/main.nf index 0f15c86c..0ec9741b 100644 --- a/modules/umitools/dedup/main.nf +++ b/modules/umitools/dedup/main.nf @@ -23,10 +23,9 @@ process UMITOOLS_DEDUP { output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def paired = meta.single_end ? "" : "--paired" """ diff --git a/modules/umitools/extract/main.nf b/modules/umitools/extract/main.nf index 0a5e6636..d90a3ba8 100644 --- a/modules/umitools/extract/main.nf +++ b/modules/umitools/extract/main.nf @@ -24,10 +24,9 @@ process UMITOOLS_EXTRACT { output: tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), path("*.log") , emit: log - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { """ diff --git a/modules/unicycler/main.nf b/modules/unicycler/main.nf index 1dd97c40..2f7c49d6 100644 --- a/modules/unicycler/main.nf +++ b/modules/unicycler/main.nf @@ -25,10 +25,9 @@ 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 "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}" """ diff --git a/modules/untar/main.nf b/modules/untar/main.nf index 0866dd55..efb9d825 100644 --- a/modules/untar/main.nf +++ b/modules/untar/main.nf @@ -23,10 +23,9 @@ process UNTAR { output: path "$untar" , emit: untar - path "versions.yml", emit: version + path "versions.yml", emit: versions script: - def software = getSoftwareName(task.process) untar = archive.toString() - '.tar.gz' """ tar \\ diff --git a/modules/unzip/main.nf b/modules/unzip/main.nf index 9e64bb1b..6530bd40 100644 --- a/modules/unzip/main.nf +++ b/modules/unzip/main.nf @@ -24,10 +24,9 @@ process UNZIP { output: path "${archive.baseName}/" , emit: unzipped_archive - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) if ( archive instanceof List && archive.name.size > 1 ) { exit 1, "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." } diff --git a/modules/variantbam/main.nf b/modules/variantbam/main.nf index c4ac3742..e73b8bf1 100644 --- a/modules/variantbam/main.nf +++ b/modules/variantbam/main.nf @@ -25,10 +25,9 @@ process VARIANTBAM { output: tuple val(meta), path("*.bam") , emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ variant \\ diff --git a/modules/vcftools/main.nf b/modules/vcftools/main.nf index a8d8969c..32607958 100644 --- a/modules/vcftools/main.nf +++ b/modules/vcftools/main.nf @@ -24,11 +24,11 @@ process VCFTOOLS { // Other optional input files can be utilised in a similar way to below but we do not exhaustively itterate through all // possible options. Instead we leave that to the user. tuple val(meta), path(variant_file) - path(bed) - path(diff_variant_file) + path bed) + path diff_variant_file output: - path("versions.yml") , emit: version + path "versions.yml", emit: versions tuple val(meta), path("*.vcf"), optional:true, emit: vcf tuple val(meta), path("*.bcf"), optional:true, emit: bcf @@ -94,7 +94,6 @@ process VCFTOOLS { tuple val(meta), path("*.diff.switch"), optional:true, emit: diff_switch_error script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def args = options.args.tokenize() diff --git a/modules/yara/index/main.nf b/modules/yara/index/main.nf index e99d99ba..51ae8a32 100644 --- a/modules/yara/index/main.nf +++ b/modules/yara/index/main.nf @@ -23,10 +23,9 @@ process YARA_INDEX { output: path "yara" , emit: index - path "versions.yml", emit: version + path "versions.yml", emit: versions script: - def software = getSoftwareName(task.process) """ mkdir yara diff --git a/modules/yara/mapper/main.nf b/modules/yara/mapper/main.nf index 88e3d411..3d69674c 100644 --- a/modules/yara/mapper/main.nf +++ b/modules/yara/mapper/main.nf @@ -24,10 +24,9 @@ process YARA_MAPPER { output: tuple val(meta), path("*.mapped.bam"), emit: bam - path "versions.yml" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { """