mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2025-01-09 23:31:13 -05:00
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line * Replace version with versions in emit statement * Fix default software names
This commit is contained in:
parent
de14533964
commit
7b3315591a
257 changed files with 271 additions and 524 deletions
modules
abacas
adapterremoval
agrvate
allelecounter
amps
arriba
artic
bamaligncleaner
bandage/image
bbmap
bcftools
concat
consensus
filter
isec
merge
mpileup
norm
query
reheader
stats
view
bedtools
bamtobed
complement
genomecov
getfasta
intersect
makewindows
maskfasta
merge
slop
sort
subtract
bismark
align
deduplicate
genomepreparation
methylationextractor
report
summary
blast
bowtie
bowtie2
bwa
bwamem2
bwameth
cat
chromap
cnvkit
cooler
custom/dumpsoftwareversions
cutadapt
damageprofiler
deeptools
delly/call
diamond
dragonflye
dshbio
ensemblvep
expansionhunter
fastani
fastp
fastqc
fasttree
fgbio
flash
gatk4
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@ -24,10 +24,9 @@ process ABACAS {
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output:
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tuple val(meta), path('*.abacas*'), emit: results
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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abacas.pl \\
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@ -23,10 +23,9 @@ process ADAPTERREMOVAL {
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output:
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tuple val(meta), path('*.fastq.gz'), emit: reads
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if (meta.single_end) {
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@ -24,10 +24,9 @@ process AGRVATE {
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output:
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tuple val(meta), path("${fasta.baseName}-results/${fasta.baseName}-summary.tab"), emit: summary
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path "${fasta.baseName}-results" , emit: results_dir
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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agrvate \\
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@ -24,10 +24,9 @@ process ALLELECOUNTER {
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output:
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tuple val(meta), path("*.alleleCount"), emit: allelecount
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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alleleCounter \\
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@ -27,7 +27,7 @@ process AMPS {
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path "results/heatmap_overview_Wevid.pdf" , emit: summary_pdf
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path "results/heatmap_overview_Wevid.tsv" , emit: tsv
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path "results/pdf_candidate_profiles/" , emit: candidate_pdfs
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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"""
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@ -41,7 +41,7 @@ process AMPS {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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amps: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
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${getSoftwareName(task.process)}: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
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END_VERSIONS
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"""
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}
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@ -26,10 +26,9 @@ process ARRIBA {
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output:
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tuple val(meta), path("*.fusions.tsv") , emit: fusions
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tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def blacklist = (options.args.contains('-b')) ? '' : '-f blacklist'
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"""
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@ -23,10 +23,9 @@ process ARTIC_GUPPYPLEX {
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output:
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tuple val(meta), path("*.fastq.gz"), emit: fastq
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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artic \\
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@ -40,10 +40,9 @@ process ARTIC_MINION {
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tuple val(meta), path("${prefix}.pass.vcf.gz") , emit: vcf
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tuple val(meta), path("${prefix}.pass.vcf.gz.tbi") , emit: tbi
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tuple val(meta), path("*.json"), optional:true , emit: json
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def version = scheme_version.toString().toLowerCase().replaceAll('v','')
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def fast5 = params.fast5_dir ? "--fast5-directory $fast5_dir" : ""
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@ -23,10 +23,9 @@ process BAMALIGNCLEANER {
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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@ -24,10 +24,9 @@ process BANDAGE_IMAGE {
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output:
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tuple val(meta), path('*.png'), emit: png
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tuple val(meta), path('*.svg'), emit: svg
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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Bandage image $gfa ${prefix}.png $options.args
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@ -24,10 +24,9 @@ process BBMAP_ALIGN {
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"
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@ -24,10 +24,9 @@ process BBMAP_BBDUK {
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output:
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tuple val(meta), path('*.fastq.gz'), emit: reads
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}"
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def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
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@ -30,10 +30,9 @@ process BBMAP_BBSPLIT {
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tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq
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tuple val(meta), path('*fastq.gz') , optional:true, emit: all_fastq
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tuple val(meta), path('*txt') , optional:true, emit: stats
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def avail_mem = 3
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@ -23,10 +23,9 @@ process BBMAP_INDEX {
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output:
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path 'ref' , emit: index
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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"""
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bbmap.sh \\
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ref=${fasta} \\
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@ -23,10 +23,9 @@ process BCFTOOLS_CONCAT {
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output:
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tuple val(meta), path("*.gz"), emit: vcf
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bcftools concat \\
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@ -23,10 +23,9 @@ process BCFTOOLS_CONSENSUS {
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output:
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tuple val(meta), path('*.fa'), emit: fasta
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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cat $fasta | bcftools consensus $vcf $options.args > ${prefix}.fa
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@ -23,10 +23,9 @@ process BCFTOOLS_FILTER {
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output:
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tuple val(meta), path("*.gz"), emit: vcf
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bcftools filter \\
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@ -23,10 +23,9 @@ process BCFTOOLS_ISEC {
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output:
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tuple val(meta), path("${prefix}"), emit: results
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bcftools isec \\
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@ -23,10 +23,9 @@ process BCFTOOLS_MERGE {
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output:
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tuple val(meta), path("*.gz"), emit: vcf
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bcftools merge -Oz \\
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@ -26,10 +26,9 @@ process BCFTOOLS_MPILEUP {
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tuple val(meta), path("*.gz") , emit: vcf
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tuple val(meta), path("*.tbi") , emit: tbi
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tuple val(meta), path("*stats.txt"), emit: stats
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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echo "${meta.id}" > sample_name.list
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@ -24,10 +24,9 @@ process BCFTOOLS_NORM {
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output:
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tuple val(meta), path("*.gz") , emit: vcf
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bcftools norm \\
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@ -26,10 +26,9 @@ process BCFTOOLS_QUERY {
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output:
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tuple val(meta), path("*.gz") , emit: vcf
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def regions_file = regions ? "--regions-file ${regions}" : ""
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def targets_file = targets ? "--targets-file ${targets}" : ""
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@ -25,10 +25,9 @@ process BCFTOOLS_REHEADER {
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def update_sequences = fai ? "-f $fai" : ""
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def new_header = header ? "-h $header" : ""
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@ -23,10 +23,9 @@ process BCFTOOLS_STATS {
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output:
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tuple val(meta), path("*stats.txt"), emit: stats
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bcftools stats $options.args $vcf > ${prefix}.bcftools_stats.txt
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@ -26,10 +26,9 @@ process BCFTOOLS_VIEW {
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output:
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tuple val(meta), path("*.gz") , emit: vcf
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def regions_file = regions ? "--regions-file ${regions}" : ""
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def targets_file = targets ? "--targets-file ${targets}" : ""
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@ -23,10 +23,9 @@ process BEDTOOLS_BAMTOBED {
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output:
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tuple val(meta), path("*.bed"), emit: bed
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools \\
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@ -24,10 +24,9 @@ process BEDTOOLS_COMPLEMENT {
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output:
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tuple val(meta), path('*.bed'), emit: bed
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools \\
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@ -25,10 +25,9 @@ process BEDTOOLS_GENOMECOV {
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output:
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tuple val(meta), path("*.${extension}"), emit: genomecov
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if (intervals.name =~ /\.bam/) {
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"""
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@ -24,10 +24,9 @@ process BEDTOOLS_GETFASTA {
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output:
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path "*.fa" , emit: fasta
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${bed.baseName}${options.suffix}" : "${bed.baseName}"
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"""
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bedtools \\
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@ -24,10 +24,9 @@ process BEDTOOLS_INTERSECT {
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output:
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tuple val(meta), path("*.${extension}"), emit: intersect
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools \\
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@ -24,10 +24,9 @@ process BEDTOOLS_MAKEWINDOWS {
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output:
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tuple val(meta), path("*.tab"), emit: tab
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def arg_input = use_bed ? "-b $regions" : "-g $regions"
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"""
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@ -24,10 +24,9 @@ process BEDTOOLS_MASKFASTA {
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output:
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tuple val(meta), path("*.fa"), emit: fasta
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools \\
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@ -23,10 +23,9 @@ process BEDTOOLS_MERGE {
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output:
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tuple val(meta), path('*.bed'), emit: bed
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools \\
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@ -24,10 +24,9 @@ process BEDTOOLS_SLOP {
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output:
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tuple val(meta), path("*.bed"), emit: bed
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
|
|
|
@ -23,10 +23,9 @@ process BEDTOOLS_SUBTRACT {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.bed"), emit: bed
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
|
|
|
@ -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 ${reads[1]}"
|
||||
"""
|
||||
|
|
|
@ -24,10 +24,9 @@ process BISMARK_DEDUPLICATE {
|
|||
output:
|
||||
tuple val(meta), path("*.deduplicated.bam") , emit: bam
|
||||
tuple val(meta), path("*.deduplication_report.txt"), emit: report
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def seqtype = meta.single_end ? '-s' : '-p'
|
||||
"""
|
||||
|
|
|
@ -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 \\
|
||||
|
|
|
@ -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 \\
|
||||
|
|
|
@ -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 $options.args
|
||||
|
||||
|
|
|
@ -26,10 +26,9 @@ process BISMARK_SUMMARY {
|
|||
|
||||
output:
|
||||
path "*report.{html,txt}", emit: summary
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
"""
|
||||
bismark2summary
|
||||
|
||||
|
|
|
@ -24,10 +24,9 @@ process BLAST_BLASTN {
|
|||
|
||||
output:
|
||||
tuple val(meta), path('*.blastn.txt'), emit: txt
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'`
|
||||
|
|
|
@ -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 $fasta \\
|
||||
|
|
|
@ -25,11 +25,10 @@ process BOWTIE_ALIGN {
|
|||
output:
|
||||
tuple val(meta), path('*.bam'), emit: bam
|
||||
tuple val(meta), path('*.out'), emit: log
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${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]}"
|
||||
|
|
|
@ -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}
|
||||
|
|
|
@ -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" : ''
|
||||
|
|
|
@ -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}
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
|
||||
if (meta.single_end) {
|
||||
|
|
|
@ -23,10 +23,9 @@ process BWA_INDEX {
|
|||
|
||||
output:
|
||||
path "bwa" , emit: index
|
||||
path "versions.yml", emit: version
|
||||
path "versions.yml", emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
"""
|
||||
mkdir bwa
|
||||
bwa \\
|
||||
|
|
|
@ -24,10 +24,9 @@ process BWA_MEM {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
|
||||
"""
|
||||
|
|
|
@ -24,10 +24,9 @@ process BWA_SAMPE {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def read_group = meta.read_group ? "-r ${meta.read_group}" : ""
|
||||
|
||||
|
|
|
@ -24,10 +24,9 @@ process BWA_SAMSE {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def read_group = meta.read_group ? "-r ${meta.read_group}" : ""
|
||||
|
||||
|
|
|
@ -23,10 +23,9 @@ process BWAMEM2_INDEX {
|
|||
|
||||
output:
|
||||
path "bwamem2" , emit: index
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
"""
|
||||
mkdir bwamem2
|
||||
bwa-mem2 \\
|
||||
|
|
|
@ -24,10 +24,9 @@ process BWAMEM2_MEM {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
|
||||
"""
|
||||
|
|
|
@ -24,10 +24,9 @@ process BWAMETH_ALIGN {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
|
||||
"""
|
||||
|
|
|
@ -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 $fasta
|
||||
|
||||
|
|
|
@ -23,7 +23,7 @@ process CAT_CAT {
|
|||
|
||||
output:
|
||||
path "${file_out}*" , emit: file_out
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def file_list = files_in.collect { it.toString() }
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
|
|
|
@ -34,10 +34,9 @@ process CHROMAP_CHROMAP {
|
|||
tuple val(meta), path("*.bam") , optional:true, emit: bam
|
||||
tuple val(meta), path("*.tagAlign.gz"), optional:true, emit: tagAlign
|
||||
tuple val(meta), path("*.pairs.gz") , optional:true, emit: pairs
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = options.args.tokenize()
|
||||
|
||||
|
|
|
@ -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 \\
|
||||
|
|
|
@ -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 \\
|
||||
|
|
|
@ -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 \\
|
||||
$options.args \\
|
||||
|
|
|
@ -23,10 +23,9 @@ process COOLER_DUMP {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.bedpe"), emit: bedpe
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
cooler dump \\
|
||||
|
|
|
@ -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:
|
||||
"""
|
||||
|
|
|
@ -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 ${prefix}_2.trim.fastq.gz"
|
||||
"""
|
||||
|
|
|
@ -25,10 +25,9 @@ process DAMAGEPROFILER {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("${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}" : "${meta.id}"
|
||||
|
||||
"""
|
||||
|
|
|
@ -25,10 +25,9 @@ process DEEPTOOLS_COMPUTEMATRIX {
|
|||
output:
|
||||
tuple val(meta), path("*.mat.gz") , emit: matrix
|
||||
tuple val(meta), path("*.mat.tab"), emit: table
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
computeMatrix \\
|
||||
|
|
|
@ -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 ${params.fragment_size}" : ''
|
||||
"""
|
||||
|
|
|
@ -24,10 +24,9 @@ process DEEPTOOLS_PLOTHEATMAP {
|
|||
output:
|
||||
tuple val(meta), path("*.pdf"), emit: pdf
|
||||
tuple val(meta), path("*.tab"), emit: table
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
plotHeatmap \\
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
"""
|
||||
plotProfile \\
|
||||
|
|
|
@ -26,10 +26,9 @@ process DELLY_CALL {
|
|||
output:
|
||||
tuple val(meta), path("*.bcf"), emit: bcf
|
||||
tuple val(meta), path("*.csi"), emit: csi
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
delly \\
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
"""
|
||||
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
|
||||
|
|
|
@ -26,10 +26,9 @@ process DIAMOND_BLASTX {
|
|||
|
||||
output:
|
||||
tuple val(meta), path('*.txt'), emit: txt
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
|
||||
|
|
|
@ -25,10 +25,9 @@ process DIAMOND_MAKEDB {
|
|||
|
||||
output:
|
||||
path "${fasta}.dmnd", emit: db
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
"""
|
||||
diamond \\
|
||||
makedb \\
|
||||
|
|
|
@ -27,10 +27,9 @@ process DRAGONFLYE {
|
|||
tuple val(meta), path("{flye,miniasm,raven}.fasta") , emit: raw_contigs
|
||||
tuple val(meta), path("{miniasm,raven}-unpolished.gfa"), optional:true , emit: gfa
|
||||
tuple val(meta), path("flye-info.txt"), optional:true , emit: txt
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def memory = task.memory.toGiga()
|
||||
"""
|
||||
dragonflye \\
|
||||
|
|
|
@ -23,10 +23,9 @@ process DSHBIO_EXPORTSEGMENTS {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.fa"), emit: fasta
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
dsh-bio \\
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
"""
|
||||
dsh-bio \\
|
||||
|
|
|
@ -23,10 +23,9 @@ process DSHBIO_FILTERGFF3 {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.gff3.gz"), emit: gff3
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
dsh-bio \\
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
"""
|
||||
dsh-bio \\
|
||||
|
|
|
@ -23,10 +23,9 @@ process DSHBIO_SPLITGFF3 {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.gff3.gz"), emit: gff3
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
dsh-bio \\
|
||||
|
|
|
@ -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"
|
||||
"""
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
def gender = (meta.gender == 'male' || meta.gender == 1 || meta.gender == 'XY') ? "male" : "female"
|
||||
"""
|
||||
|
|
|
@ -24,10 +24,9 @@ process FASTANI {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.ani.txt"), emit: ani
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
|
||||
if (meta.batch_input) {
|
||||
|
|
|
@ -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 ${prefix}.fail.fastq.gz" : ''
|
||||
|
|
|
@ -24,11 +24,11 @@ process FASTQC {
|
|||
output:
|
||||
tuple val(meta), path("*.html"), emit: html
|
||||
tuple val(meta), path("*.zip") , emit: zip
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
// Add soft-links to original FastQs for consistent naming in pipeline
|
||||
def prefix = options.suffix ? "${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
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -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 \\
|
||||
$options.args \\
|
||||
|
|
|
@ -22,10 +22,9 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
fgbio \\
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
"""
|
||||
fgbio \\
|
||||
|
|
|
@ -22,10 +22,9 @@ process FLASH {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.fastq.gz"), emit: reads
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
flash \\
|
||||
|
|
|
@ -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 ${intervals}" : ""
|
||||
"""
|
||||
|
|
|
@ -29,10 +29,9 @@ process GATK4_BASERECALIBRATOR {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.table"), emit: table
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
|
||||
def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
|
||||
|
|
|
@ -24,10 +24,9 @@ process GATK4_BEDTOINTERVALLIST {
|
|||
|
||||
output:
|
||||
tuple val(meta), path('*.interval_list'), emit: interval_list
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
gatk BedToIntervalList \\
|
||||
|
|
|
@ -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.'
|
||||
|
|
|
@ -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 ${reads[1]}"
|
||||
"""
|
||||
|
|
|
@ -26,10 +26,9 @@ process GATK4_GETPILEUPSUMMARIES {
|
|||
|
||||
output:
|
||||
tuple val(meta), path('*.pileups.table'), emit: table
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def sitesCommand = ''
|
||||
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
|
|
|
@ -23,10 +23,9 @@ process GATK4_INTERVALLISTTOOLS {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*_split/*/*.interval_list"), emit: interval_list
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
|
||||
|
|
|
@ -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}" : "${meta.id}"
|
||||
"""
|
||||
gatk MarkDuplicates \\
|
||||
|
|
|
@ -26,10 +26,9 @@ process GATK4_MERGEBAMALIGNMENT {
|
|||
|
||||
output:
|
||||
tuple val(meta), path('*.bam'), emit: bam
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
gatk MergeBamAlignment \\
|
||||
|
|
Some files were not shown because too many files have changed in this diff Show more
Loading…
Reference in a new issue