mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
Unify syntax
This commit is contained in:
drpatelh
parent
cbf8329ffd
commit
e438d026bd
28 changed files with 965 additions and 963 deletions
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@ -53,14 +53,14 @@ process SOFTWARE_TOOL {
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// e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
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tuple val(meta), path(reads)
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// TODO nf-core: List additional required input channels/values here
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val options
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val options
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output:
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// TODO nf-core: Named file extensions MUST be emitted for ALL output channels
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// TODO nf-core: If meta is provided in "input:" section then it MUST be added to ALL output channels (except version)
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tuple val(meta), path("*.bam"), emit: bam
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// TODO nf-core: List additional required output channels/values here
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -15,10 +15,10 @@ process BWA_INDEX {
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input:
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path fasta
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val options
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val options
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output:
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path "${fasta}.*", emit: index
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path "${fasta}.*" , emit: index
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path "*.version.txt", emit: version
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script:
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@ -15,23 +15,23 @@ process BWA_MEM {
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input:
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tuple val(meta), path(reads)
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path index
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path fasta
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val options
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path index
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path fasta
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val options
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def rg = meta.read_group ? "-R ${meta.read_group}" : ""
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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"""
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bwa mem \\
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$ioptions.args \\
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$rg \\
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$read_group \\
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-t $task.cpus \\
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$fasta \\
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$reads \\
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@ -15,13 +15,13 @@ process DEEPTOOLS_COMPUTEMATRIX {
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input:
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tuple val(meta), path(bigwig)
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path bed
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val options
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path bed
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val options
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output:
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tuple val(meta), path("*.mat.gz"), emit: matrix
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tuple val(meta), path("*.mat.gz") , emit: matrix
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tuple val(meta), path("*.mat.tab"), emit: table
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -15,13 +15,13 @@ process DEEPTOOLS_PLOTFINGERPRINT {
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input:
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tuple val(meta), path(bams), path(bais)
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val options
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val options
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output:
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tuple val(meta), path("*.pdf"), emit: pdf
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tuple val(meta), path("*.raw.txt"), emit: matrix
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tuple val(meta), path("*.pdf") , emit: pdf
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tuple val(meta), path("*.raw.txt") , emit: matrix
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tuple val(meta), path("*.qcmetrics.txt"), emit: metrics
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -15,12 +15,12 @@ process DEEPTOOLS_PLOTHEATMAP {
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input:
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tuple val(meta), path(matrix)
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val options
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val options
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output:
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tuple val(meta), path("*.pdf"), emit: pdf
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tuple val(meta), path("*.tab"), emit: table
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -15,17 +15,17 @@ process DEEPTOOLS_PLOTPROFILE {
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input:
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tuple val(meta), path(matrix)
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val options
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val options
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output:
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tuple val(meta), path("*.pdf"), emit: pdf
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tuple val(meta), path("*.tab"), emit: table
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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"""
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plotProfile \\
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$ioptions.args \\
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@ -15,12 +15,12 @@ process FASTQC {
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input:
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tuple val(meta), path(reads)
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val options
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val options
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output:
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tuple val(meta), path("*.html"), emit: html
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tuple val(meta), path("*.zip"), emit: zip
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path "*.version.txt", emit: version
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tuple val(meta), path("*.zip") , emit: zip
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path "*.version.txt" , emit: version
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script:
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// Add soft-links to original FastQs for consistent naming in pipeline
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@ -1,5 +1,5 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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include { saveFiles; getSoftwareName } from './functions'
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def VERSION = '2.2.0'
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@ -17,13 +17,13 @@ process HOMER_ANNOTATEPEAKS {
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input:
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tuple val(meta), path(peak)
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path fasta
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path gtf
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val options
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path fasta
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path gtf
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val options
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output:
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tuple val(meta), path("*annotatePeaks.txt"), emit: txt
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -15,16 +15,17 @@ process MACS2_CALLPEAK {
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input:
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tuple val(meta), path(ipbam), path(controlbam)
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val macs2_gsize
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val options
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val macs2_gsize
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val options
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output:
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tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
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tuple val(meta), path("*.xls"), emit: xls
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tuple val(meta), path("*.gappedPeak"), emit: gapped optional true
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tuple val(meta), path("*.bed"), emit: bed optional true
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tuple val(meta), path("*.bdg"), emit: bdg optional true
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path "*.version.txt", emit: version
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tuple val(meta), path("*.xls") , emit: xls
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path "*.version.txt" , emit: version
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tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped
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tuple val(meta), path("*.bed") , optional:true, emit: bed
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tuple val(meta), path("*.bdg") , optional:true, emit: bdg
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script:
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def software = getSoftwareName(task.process)
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@ -17,13 +17,13 @@ process PHANTOMPEAKQUALTOOLS {
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input:
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tuple val(meta), path(bam)
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val options
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val options
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output:
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tuple val(meta), path("*.out"), emit: spp
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tuple val(meta), path("*.pdf"), emit: pdf
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tuple val(meta), path("*.out") , emit: spp
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tuple val(meta), path("*.pdf") , emit: pdf
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tuple val(meta), path("*.Rdata"), emit: rdata
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -15,13 +15,13 @@ process PICARD_COLLECTMULTIPLEMETRICS {
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input:
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tuple val(meta), path(bam)
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path fasta
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val options
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path fasta
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val options
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output:
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tuple val(meta), path("*_metrics"), emit: metrics
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tuple val(meta), path("*.pdf"), emit: pdf
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path "*.version.txt", emit: version
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tuple val(meta), path("*.pdf") , emit: pdf
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -15,12 +15,12 @@ process PICARD_MARKDUPLICATES {
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input:
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tuple val(meta), path(bam)
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val options
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val options
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output:
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tuple val(meta), path("*.bam"), emit: bam
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.metrics.txt"), emit: metrics
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -15,11 +15,11 @@ process PICARD_MERGESAMFILES {
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input:
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tuple val(meta), path(bams)
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val options
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val options
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -16,23 +16,23 @@ process PRESEQ_LCEXTRAP {
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input:
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tuple val(meta), path(bam)
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val options
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val options
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output:
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tuple val(meta), path("*.ccurve.txt"), emit: ccurve
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tuple val(meta), path("*.log"), emit: log
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path "*.version.txt", emit: version
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tuple val(meta), path("*.log") , emit: log
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def pe = meta.single_end ? '' : '-pe'
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def paired_end = meta.single_end ? '' : '-pe'
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"""
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preseq \\
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lc_extrap \\
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$ioptions.args \\
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$pe \\
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$paired_end \\
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-output ${prefix}.ccurve.txt \\
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$bam
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cp .command.err ${prefix}.command.log
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@ -23,9 +23,11 @@ process QUALIMAP_RNASEQ {
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def paired_end = meta.single_end ? '' : '-pe'
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def memory = task.memory.toGiga() + "G"
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def strandedness = 'non-strand-specific'
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if (meta.strandedness == 'forward') {
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@ -33,8 +35,6 @@ process QUALIMAP_RNASEQ {
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} else if (meta.strandedness == 'reverse') {
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strandedness = 'strand-specific-reverse'
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}
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def paired_end = meta.single_end ? '' : '-pe'
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def memory = task.memory.toGiga() + "G"
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"""
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unset DISPLAY
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mkdir tmp
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@ -24,9 +24,10 @@ process SALMON_QUANT {
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def endedness = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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def strandedness = meta.single_end ? 'U' : 'IU'
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if (meta.strandedness == 'forward') {
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@ -34,7 +35,6 @@ process SALMON_QUANT {
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} else if (meta.strandedness == 'reverse') {
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strandedness = meta.single_end ? 'SR' : 'ISR'
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}
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def endedness = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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"""
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salmon quant \\
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--geneMap $gtf \\
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@ -14,11 +14,11 @@ process SAMTOOLS_FLAGSTAT {
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input:
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tuple val(meta), path(bam), path(bai)
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val options
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val options
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output:
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tuple val(meta), path("*.flagstat"), emit: flagstat
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -14,11 +14,11 @@ process SAMTOOLS_IDXSTATS {
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input:
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tuple val(meta), path(bam), path(bai)
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val options
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val options
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output:
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tuple val(meta), path("*.idxstats"), emit: idxstats
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -14,11 +14,11 @@ process SAMTOOLS_INDEX {
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input:
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tuple val(meta), path(bam)
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val options
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val options
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output:
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tuple val(meta), path("*.bai"), emit: bai
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -15,11 +15,11 @@ process SAMTOOLS_SORT {
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input:
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tuple val(meta), path(bam)
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val options
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val options
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -14,11 +14,11 @@ process SAMTOOLS_STATS {
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input:
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tuple val(meta), path(bam), path(bai)
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val options
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val options
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output:
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tuple val(meta), path("*.stats"), emit: stats
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path "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -26,7 +26,7 @@ process STAR_GENOMEGENERATE {
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def avail_mem = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
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def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
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"""
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mkdir star
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STAR \\
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@ -35,7 +35,7 @@ process STAR_GENOMEGENERATE {
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--genomeFastaFiles $fasta \\
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--sjdbGTFfile $gtf \\
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--runThreadN $task.cpus \\
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$avail_mem \\
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$memory \\
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$ioptions.args
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STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
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@ -23,9 +23,10 @@ process SUBREAD_FEATURECOUNTS {
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def paired_end = meta.single_end ? '' : '-p'
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def strandedness = 0
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if (meta.strandedness == 'forward') {
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@ -33,7 +34,6 @@ process SUBREAD_FEATURECOUNTS {
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} else if (meta.strandedness == 'reverse') {
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strandedness = 2
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}
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def paired_end = meta.single_end ? '' : '-p'
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"""
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||||
featureCounts \\
|
||||
$ioptions.args \\
|
||||
|
|
|
|||
|
|
@ -15,14 +15,15 @@ process TRIMGALORE {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
val options
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fq.gz"), emit: reads
|
||||
tuple val(meta), path("*.html"), emit: html optional true
|
||||
tuple val(meta), path("*.zip"), emit: zip optional true
|
||||
tuple val(meta), path("*.fq.gz") , emit: reads
|
||||
tuple val(meta), path("*report.txt"), emit: log
|
||||
path "*.version.txt", emit: version
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
tuple val(meta), path("*.html"), emit: html optional true
|
||||
tuple val(meta), path("*.zip") , emit: zip optional true
|
||||
|
||||
script:
|
||||
// Calculate number of --cores for TrimGalore based on value of task.cpus
|
||||
|
|
@ -37,8 +38,8 @@ process TRIMGALORE {
|
|||
}
|
||||
|
||||
// Clipping presets have to be evaluated in the context of SE/PE
|
||||
def c_r1 = params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : ''
|
||||
def c_r2 = params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : ''
|
||||
def c_r1 = params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : ''
|
||||
def c_r2 = params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : ''
|
||||
def tpc_r1 = params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : ''
|
||||
def tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
|
||||
|
||||
|
|
|
|||
|
|
@ -17,12 +17,12 @@ process UCSC_BEDRAPHTOBIGWIG {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(bedgraph)
|
||||
path sizes
|
||||
val options
|
||||
path sizes
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bigWig"), emit: bigwig
|
||||
path "*.version.txt", emit: version
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
|
|
|
|||
Loading…
Reference in a new issue