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Remove def software lines and emit versions channel as plural (#780)

Browse source 
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
This commit is contained in:
Harshil Patel 2021-10-01 14:04:56 +01:00 committed by GitHub
parent de14533964
commit 7b3315591a
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
257 changed files with 271 additions and 524 deletions
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3
modules/abacas/main.nf
View file

@ -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 \\

3
modules/adapterremoval/main.nf
View file

@ -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) {

3
modules/agrvate/main.nf
View file

@ -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 \\

3
modules/allelecounter/main.nf
View file

@ -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 \\

4
modules/amps/main.nf
View file

@ -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
"""
}

3
modules/arriba/main.nf
View file

@ -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'
"""

3
modules/artic/guppyplex/main.nf
View file

@ -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 \\

3
modules/artic/minion/main.nf
View file

@ -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" : ""

3
modules/bamaligncleaner/main.nf
View file

@ -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}"
"""

3
modules/bandage/image/main.nf
View file

@ -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

3
modules/bbmap/align/main.nf
View file

@ -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]}"

3
modules/bbmap/bbduk/main.nf
View file

@ -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"

3
modules/bbmap/bbsplit/main.nf
View file

@ -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

3
modules/bbmap/index/main.nf
View file

@ -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} \\

3
modules/bcftools/concat/main.nf
View file

@ -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 \\

3
modules/bcftools/consensus/main.nf
View file

@ -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

3
modules/bcftools/filter/main.nf
View file

@ -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 \\

3
modules/bcftools/isec/main.nf
View file

@ -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 \\

3
modules/bcftools/merge/main.nf
View file

@ -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 \\

3
modules/bcftools/mpileup/main.nf
View file

@ -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

3
modules/bcftools/norm/main.nf
View file

@ -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 \\

3
modules/bcftools/query/main.nf
View file

@ -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}" : ""

3
modules/bcftools/reheader/main.nf
View file

@ -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" : ""

3
modules/bcftools/stats/main.nf
View file

@ -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

3
modules/bcftools/view/main.nf
View file

@ -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}" : ""

3
modules/bedtools/bamtobed/main.nf
View file

@ -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 \\

3
modules/bedtools/complement/main.nf
View file

@ -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 \\

3
modules/bedtools/genomecov/main.nf
View file

@ -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/) {
"""

3
modules/bedtools/getfasta/main.nf
View file

@ -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 \\

3
modules/bedtools/intersect/main.nf
View file

@ -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 \\

3
modules/bedtools/makewindows/main.nf
View file

@ -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"
"""

3
modules/bedtools/maskfasta/main.nf
View file

@ -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 \\

3
modules/bedtools/merge/main.nf
View file

@ -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 \\

3
modules/bedtools/slop/main.nf
View file

@ -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 \\

3
modules/bedtools/sort/main.nf
View file

@ -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 \\

3
modules/bedtools/subtract/main.nf
View file

@ -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 \\

3
modules/bismark/align/main.nf
View file

@ -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]}"
"""

3
modules/bismark/deduplicate/main.nf
View file

@ -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'
"""

3
modules/bismark/genomepreparation/main.nf
View file

@ -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 \\

3
modules/bismark/methylationextractor/main.nf
View file

@ -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 \\

3
modules/bismark/report/main.nf
View file

@ -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

3
modules/bismark/summary/main.nf
View file

@ -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

3
modules/blast/blastn/main.nf
View file

@ -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//'`

3
modules/blast/makeblastdb/main.nf
View file

@ -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 \\

3
modules/bowtie/align/main.nf
View file

@ -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]}"

3
modules/bowtie/build/main.nf
View file

@ -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}

3
modules/bowtie2/align/main.nf
View file

@ -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" : ''

3
modules/bowtie2/build/main.nf
View file

@ -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}

3
modules/bwa/aln/main.nf
View file

@ -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) {

3
modules/bwa/index/main.nf
View file

@ -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 \\

3
modules/bwa/mem/main.nf
View file

@ -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}" : ""
"""

3
modules/bwa/sampe/main.nf
View file

@ -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}" : ""

3
modules/bwa/samse/main.nf
View file

@ -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}" : ""

3
modules/bwamem2/index/main.nf
View file

@ -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 \\

3
modules/bwamem2/mem/main.nf
View file

@ -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}" : ""
"""

3
modules/bwameth/align/main.nf
View file

@ -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}" : ""
"""

3
modules/bwameth/index/main.nf
View file

@ -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

2
modules/cat/cat/main.nf
View file

@ -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() }

2
modules/cat/fastq/main.nf
View file

@ -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}"

3
modules/chromap/chromap/main.nf
View file

@ -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()

3
modules/chromap/index/main.nf
View file

@ -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 \\

3
modules/cnvkit/main.nf
View file

@ -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 \\

3
modules/cooler/digest/main.nf
View file

@ -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 \\

3
modules/cooler/dump/main.nf
View file

@ -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 \\

6
modules/custom/dumpsoftwareversions/main.nf
View file

@ -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:
"""

3
modules/cutadapt/main.nf
View file

@ -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"
"""

3
modules/damageprofiler/main.nf
View file

@ -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}"
"""

3
modules/deeptools/computematrix/main.nf
View file

@ -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 \\

3
modules/deeptools/plotfingerprint/main.nf
View file

@ -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}" : ''
"""

3
modules/deeptools/plotheatmap/main.nf
View file

@ -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 \\

3
modules/deeptools/plotprofile/main.nf
View file

@ -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 \\

3
modules/delly/call/main.nf
View file

@ -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 \\

3
modules/diamond/blastp/main.nf
View file

@ -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//'`

3
modules/diamond/blastx/main.nf
View file

@ -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//'`

3
modules/diamond/makedb/main.nf
View file

@ -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 \\

3
modules/dragonflye/main.nf
View file

@ -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 \\

3
modules/dshbio/exportsegments/main.nf
View file

@ -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 \\

3
modules/dshbio/filterbed/main.nf
View file

@ -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 \\

3
modules/dshbio/filtergff3/main.nf
View file

@ -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 \\

3
modules/dshbio/splitbed/main.nf
View file

@ -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 \\

3
modules/dshbio/splitgff3/main.nf
View file

@ -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 \\

3
modules/ensemblvep/main.nf
View file

@ -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"
"""

3
modules/expansionhunter/main.nf
View file

@ -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"
"""

3
modules/fastani/main.nf
View file

@ -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) {

3
modules/fastp/main.nf
View file

@ -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" : ''

8
modules/fastqc/main.nf
View file

@ -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
"""
}

3
modules/fasttree/main.nf
View file

@ -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 \\

3
modules/fgbio/callmolecularconsensusreads/main.nf
View file

@ -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 \\

3
modules/fgbio/sortbam/main.nf
View file

@ -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 \\

3
modules/flash/main.nf
View file

@ -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 \\

3
modules/gatk4/applybqsr/main.nf
View file

@ -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}" : ""
"""

3
modules/gatk4/baserecalibrator/main.nf
View file

@ -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(' ')

3
modules/gatk4/bedtointervallist/main.nf
View file

@ -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 \\

3
modules/gatk4/createsequencedictionary/main.nf
View file

@ -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.'

3
modules/gatk4/fastqtosam/main.nf
View file

@ -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]}"
"""

3
modules/gatk4/getpileupsummaries/main.nf
View file

@ -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 = ''

3
modules/gatk4/haplotypecaller/main.nf
View file

@ -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) {

3
modules/gatk4/intervallisttools/main.nf
View file

@ -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}"
"""

3
modules/gatk4/markduplicates/main.nf
View file

@ -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 \\

3
modules/gatk4/mergebamalignment/main.nf
View file

@ -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 \\

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