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

* 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
modules
abacas
adapterremoval
agrvate
allelecounter
amps
arriba
artic
guppyplex
minion
bamaligncleaner
bandage/image
bbmap
align
bbduk
bbsplit
index
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
blastn
makeblastdb
bowtie
align
build
bowtie2
align
build
bwa
bwamem2
bwameth
align
index
cat
chromap
chromap
index
cnvkit
cooler
digest
dump
custom/dumpsoftwareversions
cutadapt
damageprofiler
deeptools
computematrix
plotfingerprint
plotheatmap
plotprofile
delly/call
diamond
blastp
blastx
makedb
dragonflye
dshbio
exportsegments
filterbed
filtergff3
splitbed
splitgff3
ensemblvep
expansionhunter
fastani
fastp
fastqc
fasttree
fgbio
callmolecularconsensusreads
sortbam
flash
gatk4
applybqsr
baserecalibrator
bedtointervallist
createsequencedictionary
fastqtosam
getpileupsummaries
haplotypecaller
intervallisttools
markduplicates
mergebamalignment

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@ -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 \\

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@ -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) {

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@ -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 \\

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@ -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 \\

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@ -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
"""
}

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@ -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'
"""

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@ -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 \\

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@ -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" : ""

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@ -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}"
"""

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@ -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

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@ -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]}"

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@ -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"

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@ -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

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@ -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} \\

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@ -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 \\

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@ -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

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@ -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 \\

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@ -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 \\

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@ -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 \\

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@ -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

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@ -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 \\

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@ -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}" : ""

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@ -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" : ""

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@ -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

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@ -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}" : ""

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@ -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 \\

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@ -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 \\

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@ -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/) {
"""

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@ -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 \\

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@ -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 \\

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@ -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"
"""

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@ -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 \\

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@ -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 \\

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@ -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 \\

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@ -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 \\

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@ -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 \\

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@ -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]}"
"""

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@ -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'
"""

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@ -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 \\

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@ -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 \\

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@ -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

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@ -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

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@ -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//'`

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@ -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 \\

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@ -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]}"

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@ -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}

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@ -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" : ''

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@ -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}

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@ -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) {

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@ -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 \\

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@ -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}" : ""
"""

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@ -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}" : ""

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@ -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}" : ""

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@ -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 \\

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@ -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}" : ""
"""

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}" : ""
"""

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

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() }

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}"

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()

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 \\

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 \\

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@ -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 \\

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 \\

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:
"""

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"
"""

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}"
"""

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 \\

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}" : ''
"""

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 \\

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 \\

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 \\

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//'`

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//'`

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 \\

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 \\

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 \\

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 \\

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 \\

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 \\

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 \\

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"
"""

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"
"""

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) {

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" : ''

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
"""
}

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 \\

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 \\

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 \\

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 \\

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}" : ""
"""

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(' ')

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 \\

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.'

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]}"
"""

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 = ''

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) {

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}"
"""

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 \\

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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