mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
commit
436e37bcd0
91 changed files with 3146 additions and 733 deletions
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
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options.args2 = args.args2 ?: ''
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options.publish_by_id = args.publish_by_id ?: false
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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@ -52,7 +52,7 @@ def saveFiles(Map args) {
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else {
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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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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@ -20,7 +20,7 @@ def initOptions(Map args) {
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options.args2 = args.args2 ?: ''
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options.publish_by_id = args.publish_by_id ?: false
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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@ -52,7 +52,7 @@ def saveFiles(Map args) {
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else {
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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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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@ -20,7 +20,7 @@ def initOptions(Map args) {
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options.args2 = args.args2 ?: ''
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options.publish_by_id = args.publish_by_id ?: false
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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@ -52,7 +52,7 @@ def saveFiles(Map args) {
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else {
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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@ -1,42 +1,42 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process BWA_MEM {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
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//container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
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conda (params.conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
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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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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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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 ${meta.read_group}" : ""
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"""
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bwa mem \\
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$ioptions.args \\
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$rg \\
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-t $task.cpus \\
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$fasta \\
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$reads \\
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| samtools view $ioptions.args2 -@ $task.cpus -bS -o ${prefix}.bam -
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echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
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"""
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}
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process BWA_MEM {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
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//container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
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conda (params.conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
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input:
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tuple val(meta), path(reads)
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path index
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path fasta
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val options
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def 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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$read_group \\
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-t $task.cpus \\
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$fasta \\
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$reads \\
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| samtools view $ioptions.args2 -@ $task.cpus -bS -o ${prefix}.bam -
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echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
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"""
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}
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@ -20,7 +20,7 @@ def initOptions(Map args) {
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options.args2 = args.args2 ?: ''
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options.publish_by_id = args.publish_by_id ?: false
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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@ -52,7 +52,7 @@ def saveFiles(Map args) {
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else {
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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@ -1,41 +1,41 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process DEEPTOOLS_COMPUTEMATRIX {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/deeptools:3.4.3--py_0"
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//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
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conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
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input:
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tuple val(meta), path(bigwig)
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path bed
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val options
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output:
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tuple val(meta), path("*.mat.gz"), emit: matrix
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tuple val(meta), path("*.mat.tab"), emit: table
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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"""
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computeMatrix \\
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$ioptions.args \\
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--regionsFileName $bed \\
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--scoreFileName $bigwig \\
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--outFileName ${prefix}.computeMatrix.mat.gz \\
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--outFileNameMatrix ${prefix}.computeMatrix.vals.mat.tab \\
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--numberOfProcessors $task.cpus
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computeMatrix --version | sed -e "s/computeMatrix //g" > ${software}.version.txt
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"""
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}
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process DEEPTOOLS_COMPUTEMATRIX {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/deeptools:3.4.3--py_0"
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//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
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conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
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input:
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tuple val(meta), path(bigwig)
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path bed
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val options
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output:
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tuple val(meta), path("*.mat.gz") , emit: matrix
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tuple val(meta), path("*.mat.tab"), emit: table
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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"""
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computeMatrix \\
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$ioptions.args \\
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--regionsFileName $bed \\
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--scoreFileName $bigwig \\
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--outFileName ${prefix}.computeMatrix.mat.gz \\
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--outFileNameMatrix ${prefix}.computeMatrix.vals.mat.tab \\
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--numberOfProcessors $task.cpus
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computeMatrix --version | sed -e "s/computeMatrix //g" > ${software}.version.txt
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"""
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}
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@ -20,7 +20,7 @@ def initOptions(Map args) {
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options.args2 = args.args2 ?: ''
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options.publish_by_id = args.publish_by_id ?: false
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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@ -52,7 +52,7 @@ def saveFiles(Map args) {
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else {
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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|
|
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@ -1,43 +1,43 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process DEEPTOOLS_PLOTFINGERPRINT {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/deeptools:3.4.3--py_0"
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||||
//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
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conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
|
||||
|
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input:
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tuple val(meta), path(bams), path(bais)
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val options
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output:
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tuple val(meta), path("*.pdf"), emit: pdf
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tuple val(meta), path("*.raw.txt"), emit: matrix
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tuple val(meta), path("*.qcmetrics.txt"), emit: metrics
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path "*.version.txt", emit: version
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|
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def extend = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : ''
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"""
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plotFingerprint \\
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$ioptions.args \\
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$extend \\
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--bamfiles ${bams.join(' ')} \\
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--plotFile ${prefix}.plotFingerprint.pdf \\
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--outRawCounts ${prefix}.plotFingerprint.raw.txt \\
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--outQualityMetrics ${prefix}.plotFingerprint.qcmetrics.txt \\
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--numberOfProcessors $task.cpus
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plotFingerprint --version | sed -e "s/plotFingerprint //g" > ${software}.version.txt
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||||
"""
|
||||
}
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// Import generic module functions
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||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process DEEPTOOLS_PLOTFINGERPRINT {
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||||
tag "$meta.id"
|
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label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/deeptools:3.4.3--py_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
|
||||
|
||||
conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams), path(bais)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.pdf") , emit: pdf
|
||||
tuple val(meta), path("*.raw.txt") , emit: matrix
|
||||
tuple val(meta), path("*.qcmetrics.txt"), emit: metrics
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def extend = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : ''
|
||||
"""
|
||||
plotFingerprint \\
|
||||
$ioptions.args \\
|
||||
$extend \\
|
||||
--bamfiles ${bams.join(' ')} \\
|
||||
--plotFile ${prefix}.plotFingerprint.pdf \\
|
||||
--outRawCounts ${prefix}.plotFingerprint.raw.txt \\
|
||||
--outQualityMetrics ${prefix}.plotFingerprint.qcmetrics.txt \\
|
||||
--numberOfProcessors $task.cpus
|
||||
|
||||
plotFingerprint --version | sed -e "s/plotFingerprint //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,38 +1,38 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process DEEPTOOLS_PLOTHEATMAP {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/deeptools:3.4.3--py_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
|
||||
|
||||
conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(matrix)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.pdf"), emit: pdf
|
||||
tuple val(meta), path("*.tab"), emit: table
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
plotHeatmap \\
|
||||
$ioptions.args \\
|
||||
--matrixFile $matrix \\
|
||||
--outFileName ${prefix}.plotHeatmap.pdf \\
|
||||
--outFileNameMatrix ${prefix}.plotHeatmap.mat.tab
|
||||
|
||||
plotHeatmap --version | sed -e "s/plotHeatmap //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process DEEPTOOLS_PLOTHEATMAP {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/deeptools:3.4.3--py_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
|
||||
|
||||
conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(matrix)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.pdf"), emit: pdf
|
||||
tuple val(meta), path("*.tab"), emit: table
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
plotHeatmap \\
|
||||
$ioptions.args \\
|
||||
--matrixFile $matrix \\
|
||||
--outFileName ${prefix}.plotHeatmap.pdf \\
|
||||
--outFileNameMatrix ${prefix}.plotHeatmap.mat.tab
|
||||
|
||||
plotHeatmap --version | sed -e "s/plotHeatmap //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,38 +1,38 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process DEEPTOOLS_PLOTPROFILE {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/deeptools:3.4.3--py_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
|
||||
|
||||
conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(matrix)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.pdf"), emit: pdf
|
||||
tuple val(meta), path("*.tab"), emit: table
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
plotProfile \\
|
||||
$ioptions.args \\
|
||||
--matrixFile $matrix \\
|
||||
--outFileName ${prefix}.plotProfile.pdf \\
|
||||
--outFileNameData ${prefix}.plotProfile.tab
|
||||
|
||||
plotProfile --version | sed -e "s/plotProfile //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process DEEPTOOLS_PLOTPROFILE {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/deeptools:3.4.3--py_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
|
||||
|
||||
conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(matrix)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.pdf"), emit: pdf
|
||||
tuple val(meta), path("*.tab"), emit: table
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
plotProfile \\
|
||||
$ioptions.args \\
|
||||
--matrixFile $matrix \\
|
||||
--outFileName ${prefix}.plotProfile.pdf \\
|
||||
--outFileNameData ${prefix}.plotProfile.tab
|
||||
|
||||
plotProfile --version | sed -e "s/plotProfile //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -15,12 +15,12 @@ process FASTQC {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
val options
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.html"), emit: html
|
||||
tuple val(meta), path("*.zip"), emit: zip
|
||||
path "*.version.txt", emit: version
|
||||
tuple val(meta), path("*.zip") , emit: zip
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
// Add soft-links to original FastQs for consistent naming in pipeline
|
||||
|
|
59
software/gffread/functions.nf
Normal file
59
software/gffread/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
30
software/gffread/main.nf
Normal file
30
software/gffread/main.nf
Normal file
|
@ -0,0 +1,30 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process GFFREAD {
|
||||
tag "$gff"
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
||||
|
||||
container "quay.io/biocontainers/gffread:0.11.7--h8b12597_0"
|
||||
//container https://depot.galaxyproject.org/singularity/gffread:0.11.7--h8b12597_0
|
||||
|
||||
conda (params.conda ? "bioconda::gffread=0.11.7" : null)
|
||||
|
||||
input:
|
||||
path gff
|
||||
val options
|
||||
|
||||
output:
|
||||
path "*.gtf" , emit: gtf
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
"""
|
||||
gffread $gff $ioptions.args -o ${gff.baseName}.gtf
|
||||
echo \$(gffread --version 2>&1) > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/hisat2/align/functions.nf
Normal file
59
software/hisat2/align/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
90
software/hisat2/align/main.nf
Normal file
90
software/hisat2/align/main.nf
Normal file
|
@ -0,0 +1,90 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
def VERSION = '2.2.0'
|
||||
|
||||
process HISAT2_ALIGN {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
|
||||
//container "https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
|
||||
|
||||
conda (params.conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path index
|
||||
path splicesites
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
tuple val(meta), path("*.log"), emit: summary
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
|
||||
def strandedness = ''
|
||||
if (meta.strandedness == 'forward') {
|
||||
strandedness = meta.single_end ? '--rna-strandness F' : '--rna-strandness FR'
|
||||
} else if (meta.strandedness == 'reverse') {
|
||||
strandedness = meta.single_end ? '--rna-strandness R' : '--rna-strandness RF'
|
||||
}
|
||||
def seq_center = params.seq_center ? "--rg-id ${prefix} --rg CN:${params.seq_center.replaceAll('\\s','_')} SM:$prefix" : "--rg-id ${prefix} --rg SM:$prefix"
|
||||
if (meta.single_end) {
|
||||
def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
|
||||
"""
|
||||
INDEX=`find -L ./ -name "*.1.ht2" | sed 's/.1.ht2//'`
|
||||
hisat2 \\
|
||||
-x \$INDEX \\
|
||||
-U $reads \\
|
||||
$strandedness \\
|
||||
--known-splicesite-infile $splicesites \\
|
||||
--summary-file ${prefix}.hisat2.summary.log \\
|
||||
--threads $task.cpus \\
|
||||
$seq_center \\
|
||||
$unaligned \\
|
||||
$ioptions.args \\
|
||||
| samtools view -bS -F 4 -F 256 - > ${prefix}.bam
|
||||
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
} else {
|
||||
def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
|
||||
"""
|
||||
INDEX=`find -L ./ -name "*.1.ht2" | sed 's/.1.ht2//'`
|
||||
hisat2 \\
|
||||
-x \$INDEX \\
|
||||
-1 ${reads[0]} \\
|
||||
-2 ${reads[1]} \\
|
||||
$strandedness \\
|
||||
--known-splicesite-infile $splicesites \\
|
||||
--summary-file ${prefix}.hisat2.summary.log \\
|
||||
--threads $task.cpus \\
|
||||
$seq_center \\
|
||||
$unaligned \\
|
||||
--no-mixed \\
|
||||
--no-discordant \\
|
||||
$ioptions.args \\
|
||||
| samtools view -bS -F 4 -F 8 -F 256 - > ${prefix}.bam
|
||||
|
||||
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
|
||||
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
|
||||
fi
|
||||
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
|
||||
mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
|
||||
fi
|
||||
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
}
|
59
software/hisat2/build/functions.nf
Normal file
59
software/hisat2/build/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
64
software/hisat2/build/main.nf
Normal file
64
software/hisat2/build/main.nf
Normal file
|
@ -0,0 +1,64 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
def VERSION = '2.2.0'
|
||||
|
||||
process HISAT2_BUILD {
|
||||
tag "$fasta"
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
||||
|
||||
container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
|
||||
//container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
|
||||
|
||||
conda (params.conda ? "bioconda::hisat2=2.2.0" : null)
|
||||
|
||||
input:
|
||||
path fasta
|
||||
path gtf
|
||||
path splicesites
|
||||
val options
|
||||
|
||||
output:
|
||||
path "hisat2", emit: index
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def avail_mem = 0
|
||||
if (!task.memory) {
|
||||
log.info "[HISAT2 index build] Available memory not known - defaulting to 0. Specify process memory requirements to change this."
|
||||
} else {
|
||||
log.info "[HISAT2 index build] Available memory: ${task.memory}"
|
||||
avail_mem = task.memory.toGiga()
|
||||
}
|
||||
|
||||
def extract_exons = ''
|
||||
def ss = ''
|
||||
def exon = ''
|
||||
if (avail_mem > params.hisat_build_memory) {
|
||||
log.info "[HISAT2 index build] Over ${params.hisat_build_memory} GB available, so using splice sites and exons in HISAT2 index"
|
||||
extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
|
||||
ss = "--ss $splicesites"
|
||||
exon = "--exon ${gtf.baseName}.exons.txt"
|
||||
} else {
|
||||
log.info "[HISAT2 index build] Less than ${params.hisat_build_memory} GB available, so NOT using splice sites and exons in HISAT2 index."
|
||||
log.info "[HISAT2 index build] Use --hisat_build_memory [small number] to skip this check."
|
||||
}
|
||||
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
"""
|
||||
mkdir hisat2
|
||||
$extract_exons
|
||||
hisat2-build \\
|
||||
-p $task.cpus \\
|
||||
$ss \\
|
||||
$exon \\
|
||||
$ioptions.args \\
|
||||
$fasta \\
|
||||
hisat2/${fasta.baseName}
|
||||
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/hisat2/extractsplicesites/functions.nf
Normal file
59
software/hisat2/extractsplicesites/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
31
software/hisat2/extractsplicesites/main.nf
Normal file
31
software/hisat2/extractsplicesites/main.nf
Normal file
|
@ -0,0 +1,31 @@
|
|||
// Import generic module functions
|
||||
include { saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
def VERSION = '2.2.0'
|
||||
|
||||
process HISAT2_EXTRACTSPLICESITES {
|
||||
tag "$gtf"
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
||||
|
||||
container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
|
||||
//container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
|
||||
|
||||
conda (params.conda ? "bioconda::hisat2=2.2.0" : null)
|
||||
|
||||
input:
|
||||
path gtf
|
||||
val options
|
||||
|
||||
output:
|
||||
path "*.splice_sites.txt", emit: txt
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
"""
|
||||
hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
}
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,43 +1,43 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
def VERSION = '4.11'
|
||||
|
||||
process HOMER_ANNOTATEPEAKS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2"
|
||||
//container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2"
|
||||
|
||||
conda (params.conda ? "bioconda::homer=4.11" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(peak)
|
||||
path fasta
|
||||
path gtf
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*annotatePeaks.txt"), emit: txt
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
annotatePeaks.pl \\
|
||||
$peak \\
|
||||
$fasta \\
|
||||
$ioptions.args \\
|
||||
-gtf $gtf \\
|
||||
-cpu $task.cpus \\
|
||||
> ${prefix}.annotatePeaks.txt
|
||||
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
def VERSION = '4.11'
|
||||
|
||||
process HOMER_ANNOTATEPEAKS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2"
|
||||
//container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2"
|
||||
|
||||
conda (params.conda ? "bioconda::homer=4.11" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(peak)
|
||||
path fasta
|
||||
path gtf
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*annotatePeaks.txt"), emit: txt
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
annotatePeaks.pl \\
|
||||
$peak \\
|
||||
$fasta \\
|
||||
$ioptions.args \\
|
||||
-gtf $gtf \\
|
||||
-cpu $task.cpus \\
|
||||
> ${prefix}.annotatePeaks.txt
|
||||
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,47 +1,48 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process MACS2_CALLPEAK {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py37h516909a_0"
|
||||
|
||||
conda (params.conda ? "bioconda::macs2=2.2.7.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(ipbam), path(controlbam)
|
||||
val macs2_gsize
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
|
||||
tuple val(meta), path("*.xls"), emit: xls
|
||||
tuple val(meta), path("*.gappedPeak"), emit: gapped optional true
|
||||
tuple val(meta), path("*.bed"), emit: bed optional true
|
||||
tuple val(meta), path("*.bdg"), emit: bdg optional true
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def format = meta.single_end ? 'BAM' : 'BAMPE'
|
||||
def control = controlbam ? "--control $controlbam" : ''
|
||||
"""
|
||||
macs2 \\
|
||||
callpeak \\
|
||||
$ioptions.args \\
|
||||
--gsize $macs2_gsize \\
|
||||
--format $format \\
|
||||
--name $prefix \\
|
||||
--treatment $ipbam \\
|
||||
$control
|
||||
|
||||
macs2 --version | sed -e "s/macs2 //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process MACS2_CALLPEAK {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py37h516909a_0"
|
||||
|
||||
conda (params.conda ? "bioconda::macs2=2.2.7.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(ipbam), path(controlbam)
|
||||
val macs2_gsize
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
|
||||
tuple val(meta), path("*.xls") , emit: xls
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped
|
||||
tuple val(meta), path("*.bed") , optional:true, emit: bed
|
||||
tuple val(meta), path("*.bdg") , optional:true, emit: bdg
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def format = meta.single_end ? 'BAM' : 'BAMPE'
|
||||
def control = controlbam ? "--control $controlbam" : ''
|
||||
"""
|
||||
macs2 \\
|
||||
callpeak \\
|
||||
$ioptions.args \\
|
||||
--gsize $macs2_gsize \\
|
||||
--format $format \\
|
||||
--name $prefix \\
|
||||
--treatment $ipbam \\
|
||||
$control
|
||||
|
||||
macs2 --version | sed -e "s/macs2 //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
59
software/macs2/functions.nf
Normal file
59
software/macs2/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,37 +1,37 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
def VERSION = '1.2.2'
|
||||
|
||||
process PHANTOMPEAKQUALTOOLS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
|
||||
|
||||
conda (params.conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.out"), emit: spp
|
||||
tuple val(meta), path("*.pdf"), emit: pdf
|
||||
tuple val(meta), path("*.Rdata"), emit: rdata
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
RUN_SPP=`which run_spp.R`
|
||||
Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
def VERSION = '1.2.2'
|
||||
|
||||
process PHANTOMPEAKQUALTOOLS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
|
||||
|
||||
conda (params.conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.out") , emit: spp
|
||||
tuple val(meta), path("*.pdf") , emit: pdf
|
||||
tuple val(meta), path("*.Rdata"), emit: rdata
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
RUN_SPP=`which run_spp.R`
|
||||
Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,47 +1,47 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process PICARD_COLLECTMULTIPLEMETRICS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/picard:2.23.2--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
|
||||
|
||||
conda (params.conda ? "bioconda::picard=2.23.2" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path fasta
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_metrics"), emit: metrics
|
||||
tuple val(meta), path("*.pdf"), emit: pdf
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
"""
|
||||
picard \\
|
||||
-Xmx${avail_mem}g \\
|
||||
CollectMultipleMetrics \\
|
||||
$ioptions.args \\
|
||||
INPUT=$bam \\
|
||||
OUTPUT=${prefix}.CollectMultipleMetrics \\
|
||||
REFERENCE_SEQUENCE=$fasta
|
||||
|
||||
echo \$(picard CollectMultipleMetrics --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process PICARD_COLLECTMULTIPLEMETRICS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/picard:2.23.2--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
|
||||
|
||||
conda (params.conda ? "bioconda::picard=2.23.2" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path fasta
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_metrics"), emit: metrics
|
||||
tuple val(meta), path("*.pdf") , emit: pdf
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
"""
|
||||
picard \\
|
||||
-Xmx${avail_mem}g \\
|
||||
CollectMultipleMetrics \\
|
||||
$ioptions.args \\
|
||||
INPUT=$bam \\
|
||||
OUTPUT=${prefix}.CollectMultipleMetrics \\
|
||||
REFERENCE_SEQUENCE=$fasta
|
||||
|
||||
echo \$(picard CollectMultipleMetrics --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,46 +1,46 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process PICARD_MARKDUPLICATES {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/picard:2.23.2--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
|
||||
|
||||
conda (params.conda ? "bioconda::picard=2.23.2" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
tuple val(meta), path("*.metrics.txt"), emit: metrics
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
"""
|
||||
picard \\
|
||||
-Xmx${avail_mem}g \\
|
||||
MarkDuplicates \\
|
||||
$ioptions.args \\
|
||||
INPUT=$bam \\
|
||||
OUTPUT=${prefix}.bam \\
|
||||
METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt
|
||||
|
||||
echo \$(picard MarkDuplicates --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process PICARD_MARKDUPLICATES {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/picard:2.23.2--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
|
||||
|
||||
conda (params.conda ? "bioconda::picard=2.23.2" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam") , emit: bam
|
||||
tuple val(meta), path("*.metrics.txt"), emit: metrics
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
"""
|
||||
picard \\
|
||||
-Xmx${avail_mem}g \\
|
||||
MarkDuplicates \\
|
||||
$ioptions.args \\
|
||||
INPUT=$bam \\
|
||||
OUTPUT=${prefix}.bam \\
|
||||
METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt
|
||||
|
||||
echo \$(picard MarkDuplicates --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,51 +1,51 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process PICARD_MERGESAMFILES {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/picard:2.23.2--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
|
||||
|
||||
conda (params.conda ? "bioconda::picard=2.23.2" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def bam_files = bams.sort()
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard MergeSamFiles] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
if (bam_files.size() > 1) {
|
||||
"""
|
||||
picard \\
|
||||
-Xmx${avail_mem}g \\
|
||||
MergeSamFiles \\
|
||||
$ioptions.args \\
|
||||
${'INPUT='+bam_files.join(' INPUT=')} \\
|
||||
OUTPUT=${prefix}.bam
|
||||
echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
ln -s ${bam_files[0]} ${prefix}.bam
|
||||
echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process PICARD_MERGESAMFILES {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/picard:2.23.2--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
|
||||
|
||||
conda (params.conda ? "bioconda::picard=2.23.2" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def bam_files = bams.sort()
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard MergeSamFiles] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
if (bam_files.size() > 1) {
|
||||
"""
|
||||
picard \\
|
||||
-Xmx${avail_mem}g \\
|
||||
MergeSamFiles \\
|
||||
$ioptions.args \\
|
||||
${'INPUT='+bam_files.join(' INPUT=')} \\
|
||||
OUTPUT=${prefix}.bam
|
||||
echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
ln -s ${bam_files[0]} ${prefix}.bam
|
||||
echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,42 +1,42 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process PRESEQ_LCEXTRAP {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
label 'error_ignore'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3"
|
||||
//container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
|
||||
|
||||
conda (params.conda ? "bioconda::preseq=2.0.3" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.ccurve.txt"), emit: ccurve
|
||||
tuple val(meta), path("*.log"), emit: log
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def pe = meta.single_end ? '' : '-pe'
|
||||
"""
|
||||
preseq \\
|
||||
lc_extrap \\
|
||||
$ioptions.args \\
|
||||
$pe \\
|
||||
-output ${prefix}.ccurve.txt \\
|
||||
$bam
|
||||
cp .command.err ${prefix}.command.log
|
||||
|
||||
echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process PRESEQ_LCEXTRAP {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
label 'error_ignore'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3"
|
||||
//container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
|
||||
|
||||
conda (params.conda ? "bioconda::preseq=2.0.3" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.ccurve.txt"), emit: ccurve
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def paired_end = meta.single_end ? '' : '-pe'
|
||||
"""
|
||||
preseq \\
|
||||
lc_extrap \\
|
||||
$ioptions.args \\
|
||||
$paired_end \\
|
||||
-output ${prefix}.ccurve.txt \\
|
||||
$bam
|
||||
cp .command.err ${prefix}.command.log
|
||||
|
||||
echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
59
software/qualimap/rnaseq/functions.nf
Normal file
59
software/qualimap/rnaseq/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
54
software/qualimap/rnaseq/main.nf
Normal file
54
software/qualimap/rnaseq/main.nf
Normal file
|
@ -0,0 +1,54 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process QUALIMAP_RNASEQ {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/qualimap:2.2.2d--1"
|
||||
//container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
|
||||
|
||||
conda (params.conda ? "bioconda::qualimap=2.2.2d" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path gtf
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}"), emit: results
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def paired_end = meta.single_end ? '' : '-pe'
|
||||
def memory = task.memory.toGiga() + "G"
|
||||
|
||||
def strandedness = 'non-strand-specific'
|
||||
if (meta.strandedness == 'forward') {
|
||||
strandedness = 'strand-specific-forward'
|
||||
} else if (meta.strandedness == 'reverse') {
|
||||
strandedness = 'strand-specific-reverse'
|
||||
}
|
||||
"""
|
||||
unset DISPLAY
|
||||
mkdir tmp
|
||||
export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
|
||||
qualimap \\
|
||||
--java-mem-size=$memory \\
|
||||
rnaseq \\
|
||||
$ioptions.args \\
|
||||
-bam $bam \\
|
||||
-gtf $gtf \\
|
||||
-p $strandedness \\
|
||||
$paired_end \\
|
||||
-outdir $prefix
|
||||
|
||||
echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/rsem/calculateexpression/functions.nf
Normal file
59
software/rsem/calculateexpression/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
49
software/rsem/calculateexpression/main.nf
Normal file
49
software/rsem/calculateexpression/main.nf
Normal file
|
@ -0,0 +1,49 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process RSEM_CALCULATEEXPRESSION {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/rsem:1.3.3--pl526ha52163a_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/rsem:1.3.3--pl526ha52163a_0"
|
||||
|
||||
conda (params.conda ? "bioconda::rsem=1.3.3" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path index
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.genes.results") , emit: counts_gene
|
||||
tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
|
||||
tuple val(meta), path("*.stat") , emit: stat
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star
|
||||
tuple val(meta), path("${prefix}.genome.bam") , optional:true, emit: bam_genome
|
||||
tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def paired_end = meta.single_end ? "" : "--paired-end"
|
||||
"""
|
||||
INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
|
||||
rsem-calculate-expression \\
|
||||
--num-threads $task.cpus \\
|
||||
--temporary-folder ./tmp/ \\
|
||||
$paired_end \\
|
||||
$ioptions.args \\
|
||||
$reads \\
|
||||
\$INDEX \\
|
||||
$prefix
|
||||
|
||||
rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/rsem/preparereference/functions.nf
Normal file
59
software/rsem/preparereference/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
39
software/rsem/preparereference/main.nf
Normal file
39
software/rsem/preparereference/main.nf
Normal file
|
@ -0,0 +1,39 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process RSEM_PREPAREREFERENCE {
|
||||
tag "$fasta"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
||||
|
||||
container "quay.io/biocontainers/rsem:1.3.3--pl526ha52163a_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/rsem:1.3.3--pl526ha52163a_0"
|
||||
|
||||
conda (params.conda ? "bioconda::rsem=1.3.3" : null)
|
||||
|
||||
input:
|
||||
path fasta
|
||||
path gtf
|
||||
val options
|
||||
|
||||
output:
|
||||
path "rsem" , emit: index
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
"""
|
||||
mkdir rsem
|
||||
rsem-prepare-reference \\
|
||||
--gtf $gtf \\
|
||||
--num-threads $task.cpus \\
|
||||
$ioptions.args \\
|
||||
$fasta \\
|
||||
rsem/genome
|
||||
|
||||
rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/rseqc/bamstat/functions.nf
Normal file
59
software/rseqc/bamstat/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
36
software/rseqc/bamstat/main.nf
Normal file
36
software/rseqc/bamstat/main.nf
Normal file
|
@ -0,0 +1,36 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process RSEQC_BAMSTAT {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
|
||||
|
||||
conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam_stat.txt"), emit: txt
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bam_stat.py \\
|
||||
-i $bam \\
|
||||
$ioptions.args \\
|
||||
> ${prefix}.bam_stat.txt
|
||||
|
||||
bam_stat.py --version | sed -e "s/bam_stat.py //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/rseqc/inferexperiment/functions.nf
Normal file
59
software/rseqc/inferexperiment/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
38
software/rseqc/inferexperiment/main.nf
Normal file
38
software/rseqc/inferexperiment/main.nf
Normal file
|
@ -0,0 +1,38 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process RSEQC_INFEREXPERIMENT {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
|
||||
|
||||
conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path bed
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.infer_experiment.txt"), emit: txt
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
infer_experiment.py \\
|
||||
-i $bam \\
|
||||
-r $bed \\
|
||||
$ioptions.args \\
|
||||
> ${prefix}.infer_experiment.txt
|
||||
|
||||
infer_experiment.py --version | sed -e "s/infer_experiment.py //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/rseqc/innerdistance/functions.nf
Normal file
59
software/rseqc/innerdistance/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
50
software/rseqc/innerdistance/main.nf
Normal file
50
software/rseqc/innerdistance/main.nf
Normal file
|
@ -0,0 +1,50 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process RSEQC_INNERDISTANCE {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
|
||||
|
||||
conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path bed
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*distance.txt"), optional:true, emit: distance
|
||||
tuple val(meta), path("*freq.txt") , optional:true, emit: freq
|
||||
tuple val(meta), path("*mean.txt") , optional:true, emit: mean
|
||||
tuple val(meta), path("*.pdf") , optional:true, emit: pdf
|
||||
tuple val(meta), path("*.r") , optional:true, emit: rscript
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
if (!meta.single_end) {
|
||||
"""
|
||||
inner_distance.py \\
|
||||
-i $bam \\
|
||||
-r $bed \\
|
||||
-o $prefix \\
|
||||
$ioptions.args \\
|
||||
> stdout.txt
|
||||
head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt
|
||||
|
||||
inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
}
|
59
software/rseqc/junctionannotation/functions.nf
Normal file
59
software/rseqc/junctionannotation/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
45
software/rseqc/junctionannotation/main.nf
Normal file
45
software/rseqc/junctionannotation/main.nf
Normal file
|
@ -0,0 +1,45 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process RSEQC_JUNCTIONANNOTATION {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
|
||||
|
||||
conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path bed
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.junction.bed"), emit: bed
|
||||
tuple val(meta), path("*.Interact.bed"), emit: interact_bed
|
||||
tuple val(meta), path("*.xls") , emit: xls
|
||||
tuple val(meta), path("*junction.pdf") , emit: pdf
|
||||
tuple val(meta), path("*events.pdf") , emit: events_pdf
|
||||
tuple val(meta), path("*.r") , emit: rscript
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
junction_annotation.py \\
|
||||
-i $bam \\
|
||||
-r $bed \\
|
||||
-o $prefix \\
|
||||
$ioptions.args \\
|
||||
2> ${prefix}.junction_annotation.log
|
||||
|
||||
junction_annotation.py --version | sed -e "s/junction_annotation.py //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/rseqc/junctionsaturation/functions.nf
Normal file
59
software/rseqc/junctionsaturation/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
39
software/rseqc/junctionsaturation/main.nf
Normal file
39
software/rseqc/junctionsaturation/main.nf
Normal file
|
@ -0,0 +1,39 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process RSEQC_JUNCTIONSATURATION {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
|
||||
|
||||
conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path bed
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.pdf"), emit: pdf
|
||||
tuple val(meta), path("*.r") , emit: rscript
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
junction_saturation.py \\
|
||||
-i $bam \\
|
||||
-r $bed \\
|
||||
-o $prefix \\
|
||||
$ioptions.args
|
||||
|
||||
junction_saturation.py --version | sed -e "s/junction_saturation.py //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/rseqc/readdistribution/functions.nf
Normal file
59
software/rseqc/readdistribution/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
37
software/rseqc/readdistribution/main.nf
Normal file
37
software/rseqc/readdistribution/main.nf
Normal file
|
@ -0,0 +1,37 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process RSEQC_READDISTRIBUTION {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
|
||||
|
||||
conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path bed
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.read_distribution.txt"), emit: txt
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
read_distribution.py \\
|
||||
-i $bam \\
|
||||
-r $bed \\
|
||||
> ${prefix}.read_distribution.txt
|
||||
|
||||
read_distribution.py --version | sed -e "s/read_distribution.py //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/rseqc/readduplication/functions.nf
Normal file
59
software/rseqc/readduplication/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
39
software/rseqc/readduplication/main.nf
Normal file
39
software/rseqc/readduplication/main.nf
Normal file
|
@ -0,0 +1,39 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process RSEQC_READDUPLICATION {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
|
||||
|
||||
conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*seq.DupRate.xls"), emit: seq_xls
|
||||
tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls
|
||||
tuple val(meta), path("*.pdf") , emit: pdf
|
||||
tuple val(meta), path("*.r") , emit: rscript
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
read_duplication.py \\
|
||||
-i $bam \\
|
||||
-o $prefix \\
|
||||
$ioptions.args
|
||||
|
||||
read_duplication.py --version | sed -e "s/read_duplication.py //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/salmon/index/functions.nf
Normal file
59
software/salmon/index/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
36
software/salmon/index/main.nf
Normal file
36
software/salmon/index/main.nf
Normal file
|
@ -0,0 +1,36 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process SALMON_INDEX {
|
||||
tag "$fasta"
|
||||
label "process_medium"
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
||||
|
||||
container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
|
||||
|
||||
conda (params.conda ? "bioconda::salmon=1.3.0" : null)
|
||||
|
||||
input:
|
||||
path fasta
|
||||
val options
|
||||
|
||||
output:
|
||||
path "salmon" , emit: index
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
"""
|
||||
salmon \\
|
||||
index \\
|
||||
--threads $task.cpus \\
|
||||
-t $fasta \\
|
||||
$ioptions.args \\
|
||||
-i salmon
|
||||
salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/salmon/quant/functions.nf
Normal file
59
software/salmon/quant/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
50
software/salmon/quant/main.nf
Normal file
50
software/salmon/quant/main.nf
Normal file
|
@ -0,0 +1,50 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process SALMON_QUANT {
|
||||
tag "$meta.id"
|
||||
label "process_medium"
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
|
||||
|
||||
conda (params.conda ? "bioconda::salmon=1.3.0" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path index
|
||||
path gtf
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}"), emit: results
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def endedness = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
|
||||
|
||||
def strandedness = meta.single_end ? 'U' : 'IU'
|
||||
if (meta.strandedness == 'forward') {
|
||||
strandedness = meta.single_end ? 'SF' : 'ISF'
|
||||
} else if (meta.strandedness == 'reverse') {
|
||||
strandedness = meta.single_end ? 'SR' : 'ISR'
|
||||
}
|
||||
"""
|
||||
salmon quant \\
|
||||
--geneMap $gtf \\
|
||||
--threads $task.cpus \\
|
||||
--libType=$strandedness \\
|
||||
--index $index \\
|
||||
$endedness \\
|
||||
$ioptions.args \\
|
||||
-o $prefix
|
||||
|
||||
salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -14,11 +14,11 @@ process SAMTOOLS_FLAGSTAT {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
val options
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.flagstat"), emit: flagstat
|
||||
path "*.version.txt", emit: version
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -14,11 +14,11 @@ process SAMTOOLS_IDXSTATS {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
val options
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.idxstats"), emit: idxstats
|
||||
path "*.version.txt", emit: version
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -14,11 +14,11 @@ process SAMTOOLS_INDEX {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bai"), emit: bai
|
||||
path "*.version.txt", emit: version
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -15,11 +15,11 @@ process SAMTOOLS_SORT {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
val options
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "*.version.txt", emit: version
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -14,11 +14,11 @@ process SAMTOOLS_STATS {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
val options
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.stats"), emit: stats
|
||||
path "*.version.txt", emit: version
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
|
|
59
software/sortmerna/functions.nf
Normal file
59
software/sortmerna/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
70
software/sortmerna/main.nf
Normal file
70
software/sortmerna/main.nf
Normal file
|
@ -0,0 +1,70 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process SORTMERNA {
|
||||
tag "$meta.id"
|
||||
label "process_high"
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/sortmerna:4.2.0--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
|
||||
|
||||
conda (params.conda ? "bioconda::sortmerna=4.2.0" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path fasta
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fastq.gz"), emit: reads
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
|
||||
def Refs = ""
|
||||
for (i=0; i<fasta.size(); i++) { Refs+= " --ref ${fasta[i]}" }
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
sortmerna \\
|
||||
$Refs \\
|
||||
--reads $reads \\
|
||||
--threads $task.cpus \\
|
||||
--workdir . \\
|
||||
--aligned rRNA_reads \\
|
||||
--other non_rRNA_reads \\
|
||||
$ioptions.args
|
||||
|
||||
gzip -f < non_rRNA_reads.fq > ${prefix}.fastq.gz
|
||||
mv rRNA_reads.log ${prefix}.sortmerna.log
|
||||
|
||||
echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
sortmerna \\
|
||||
$Refs \\
|
||||
--reads ${reads[0]} \\
|
||||
--reads ${reads[1]} \\
|
||||
--threads $task.cpus \\
|
||||
--workdir . \\
|
||||
--aligned rRNA_reads \\
|
||||
--other non_rRNA_reads \\
|
||||
--paired_in \\
|
||||
--out2 \\
|
||||
$ioptions.args
|
||||
|
||||
gzip -f < non_rRNA_reads_fwd.fq > ${prefix}_1.fastq.gz
|
||||
gzip -f < non_rRNA_reads_rev.fq > ${prefix}_2.fastq.gz
|
||||
mv rRNA_reads.log ${prefix}.sortmerna.log
|
||||
|
||||
echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
}
|
59
software/star/align/functions.nf
Normal file
59
software/star/align/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
62
software/star/align/main.nf
Normal file
62
software/star/align/main.nf
Normal file
|
@ -0,0 +1,62 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process STAR_ALIGN {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
// Don't upgrade me - 2.7X indices incompatible with iGenomes.
|
||||
container "quay.io/biocontainers/star:2.6.1d--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
|
||||
|
||||
conda (params.conda ? "bioconda::star=2.6.1d" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path index
|
||||
path gtf
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*Aligned.out.bam") , emit: bam
|
||||
tuple val(meta), path("*Log.final.out") , emit: log_final
|
||||
tuple val(meta), path("*Log.out") , emit: log_out
|
||||
tuple val(meta), path("*Log.progress.out"), emit: log_progress
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
tuple val(meta), path("*sortedByCoord.out.bam") , optional:true, emit: bam_sorted
|
||||
tuple val(meta), path("*toTranscriptome.out.bam"), optional:true, emit: bam_transcript
|
||||
tuple val(meta), path("*fastq.gz") , optional:true, emit: fastq
|
||||
tuple val(meta), path("*.tab") , optional:true, emit: tab
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
|
||||
def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix'" : "--outSAMattrRGline ID:$prefix 'SM:$prefix'"
|
||||
"""
|
||||
STAR \\
|
||||
--genomeDir $index \\
|
||||
--readFilesIn $reads \\
|
||||
--runThreadN $task.cpus \\
|
||||
--outFileNamePrefix $prefix. \\
|
||||
$ignore_gtf \\
|
||||
$seq_center \\
|
||||
$ioptions.args
|
||||
|
||||
if [ -f ${prefix}.Unmapped.out.mate1 ]; then
|
||||
mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
|
||||
gzip ${prefix}.unmapped_1.fastq
|
||||
fi
|
||||
if [ -f ${prefix}.Unmapped.out.mate2 ]; then
|
||||
mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
|
||||
gzip ${prefix}.unmapped_2.fastq
|
||||
fi
|
||||
|
||||
STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/star/genomegenerate/functions.nf
Normal file
59
software/star/genomegenerate/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
43
software/star/genomegenerate/main.nf
Normal file
43
software/star/genomegenerate/main.nf
Normal file
|
@ -0,0 +1,43 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process STAR_GENOMEGENERATE {
|
||||
tag "$fasta"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
||||
|
||||
// Don't upgrade me - 2.7X indices incompatible with iGenomes.
|
||||
container "quay.io/biocontainers/star:2.6.1d--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
|
||||
|
||||
conda (params.conda ? "bioconda::star=2.6.1d" : null)
|
||||
|
||||
input:
|
||||
path fasta
|
||||
path gtf
|
||||
val options
|
||||
|
||||
output:
|
||||
path "star" , emit: index
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
|
||||
"""
|
||||
mkdir star
|
||||
STAR \\
|
||||
--runMode genomeGenerate \\
|
||||
--genomeDir star/ \\
|
||||
--genomeFastaFiles $fasta \\
|
||||
--sjdbGTFfile $gtf \\
|
||||
--runThreadN $task.cpus \\
|
||||
$memory \\
|
||||
$ioptions.args
|
||||
|
||||
STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/stringtie/functions.nf
Normal file
59
software/stringtie/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
52
software/stringtie/main.nf
Normal file
52
software/stringtie/main.nf
Normal file
|
@ -0,0 +1,52 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process STRINGTIE {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/stringtie:2.1.2--h7e0af3c_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/stringtie:2.1.2--h7e0af3c_1"
|
||||
|
||||
conda (params.conda ? "bioconda::stringtie=2.1.2" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path gtf
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.coverage.gtf") , emit: coverage_gtf
|
||||
tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf
|
||||
tuple val(meta), path("*.txt") , emit: abundance
|
||||
tuple val(meta), path("*.ballgown") , emit: ballgown
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
|
||||
def strandedness = ''
|
||||
if (meta.strandedness == 'forward') {
|
||||
strandedness = '--fr'
|
||||
} else if (meta.strandedness == 'reverse') {
|
||||
strandedness = '--rf'
|
||||
}
|
||||
"""
|
||||
stringtie \\
|
||||
$bam \\
|
||||
$strandedness \\
|
||||
-G $gtf \\
|
||||
-o ${prefix}.transcripts.gtf \\
|
||||
-A ${prefix}.gene_abundance.txt \\
|
||||
-C ${prefix}.coverage.gtf \\
|
||||
-b ${prefix}.ballgown \\
|
||||
$ioptions.args
|
||||
|
||||
stringtie --version > ${software}.version.txt
|
||||
"""
|
||||
}
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,41 +1,49 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process SUBREAD_FEATURECOUNTS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
|
||||
|
||||
conda (params.conda ? "bioconda::subread=2.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams), path(annotation)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*featureCounts.txt"), emit: txt
|
||||
tuple val(meta), path("*featureCounts.txt.summary"), emit: summary
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def pe = meta.single_end ? '' : '-p'
|
||||
"""
|
||||
featureCounts \\
|
||||
$ioptions.args \\
|
||||
$pe \\
|
||||
-T $task.cpus \\
|
||||
-a $annotation \\
|
||||
-o ${prefix}.featureCounts.txt \\
|
||||
${bams.join(' ')}
|
||||
|
||||
echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process SUBREAD_FEATURECOUNTS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
|
||||
//container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
|
||||
|
||||
conda (params.conda ? "bioconda::subread=2.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams), path(annotation)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*featureCounts.txt") , emit: counts
|
||||
tuple val(meta), path("*featureCounts.txt.summary"), emit: summary
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
def paired_end = meta.single_end ? '' : '-p'
|
||||
|
||||
def strandedness = 0
|
||||
if (meta.strandedness == 'forward') {
|
||||
strandedness = 1
|
||||
} else if (meta.strandedness == 'reverse') {
|
||||
strandedness = 2
|
||||
}
|
||||
"""
|
||||
featureCounts \\
|
||||
$ioptions.args \\
|
||||
$paired_end \\
|
||||
-T $task.cpus \\
|
||||
-a $annotation \\
|
||||
-s $strandedness \\
|
||||
-o ${prefix}.featureCounts.txt \\
|
||||
${bams.join(' ')}
|
||||
|
||||
echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,79 +1,80 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process TRIMGALORE {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/trim-galore:0.6.5--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.5--0"
|
||||
|
||||
conda (params.conda ? "bioconda::trim-galore=0.6.5" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
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("*report.txt"), emit: log
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
// Calculate number of --cores for TrimGalore based on value of task.cpus
|
||||
// See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
|
||||
// See: https://github.com/nf-core/atacseq/pull/65
|
||||
def cores = 1
|
||||
if (task.cpus) {
|
||||
cores = (task.cpus as int) - 4
|
||||
if (meta.single_end) cores = (task.cpus as int) - 3
|
||||
if (cores < 1) cores = 1
|
||||
if (cores > 4) cores = 4
|
||||
}
|
||||
|
||||
// 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 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 ${params.three_prime_clip_r2}" : ''
|
||||
|
||||
// Added soft-links to original fastqs for consistent naming in MultiQC
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
|
||||
trim_galore \\
|
||||
$ioptions.args \\
|
||||
--cores $cores \\
|
||||
--gzip \\
|
||||
$c_r1 \\
|
||||
$tpc_r1 \\
|
||||
${prefix}.fastq.gz
|
||||
echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
|
||||
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
|
||||
trim_galore \\
|
||||
$ioptions.args \\
|
||||
--cores $cores \\
|
||||
--paired \\
|
||||
--gzip \\
|
||||
$c_r1 \\
|
||||
$c_r2 \\
|
||||
$tpc_r1 \\
|
||||
$tpc_r2 \\
|
||||
${prefix}_1.fastq.gz \\
|
||||
${prefix}_2.fastq.gz
|
||||
echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process TRIMGALORE {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/trim-galore:0.6.5--0"
|
||||
//container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.5--0"
|
||||
|
||||
conda (params.conda ? "bioconda::trim-galore=0.6.5" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fq.gz") , emit: reads
|
||||
tuple val(meta), path("*report.txt"), emit: log
|
||||
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
|
||||
// See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
|
||||
// See: https://github.com/nf-core/atacseq/pull/65
|
||||
def cores = 1
|
||||
if (task.cpus) {
|
||||
cores = (task.cpus as int) - 4
|
||||
if (meta.single_end) cores = (task.cpus as int) - 3
|
||||
if (cores < 1) cores = 1
|
||||
if (cores > 4) cores = 4
|
||||
}
|
||||
|
||||
// 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 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 ${params.three_prime_clip_r2}" : ''
|
||||
|
||||
// Added soft-links to original fastqs for consistent naming in MultiQC
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
|
||||
trim_galore \\
|
||||
$ioptions.args \\
|
||||
--cores $cores \\
|
||||
--gzip \\
|
||||
$c_r1 \\
|
||||
$tpc_r1 \\
|
||||
${prefix}.fastq.gz
|
||||
echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
|
||||
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
|
||||
trim_galore \\
|
||||
$ioptions.args \\
|
||||
--cores $cores \\
|
||||
--paired \\
|
||||
--gzip \\
|
||||
$c_r1 \\
|
||||
$c_r2 \\
|
||||
$tpc_r1 \\
|
||||
$tpc_r2 \\
|
||||
${prefix}_1.fastq.gz \\
|
||||
${prefix}_2.fastq.gz
|
||||
echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@ def initOptions(Map args) {
|
|||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = (args.publish_files instanceof Map) ? args.publish_files : null
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
@ -52,7 +52,7 @@ def saveFiles(Map args) {
|
|||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,35 +1,35 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
def VERSION = '377'
|
||||
|
||||
process UCSC_BEDRAPHTOBIGWIG {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
|
||||
|
||||
conda (params.conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bedgraph)
|
||||
path sizes
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bigWig"), emit: bigwig
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
def VERSION = '377'
|
||||
|
||||
process UCSC_BEDRAPHTOBIGWIG {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
|
||||
|
||||
conda (params.conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bedgraph)
|
||||
path sizes
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bigWig"), emit: bigwig
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig
|
||||
echo $VERSION > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
59
software/umitools/dedup/functions.nf
Normal file
59
software/umitools/dedup/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
38
software/umitools/dedup/main.nf
Normal file
38
software/umitools/dedup/main.nf
Normal file
|
@ -0,0 +1,38 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process UMITOOLS_DEDUP {
|
||||
tag "$meta.id"
|
||||
label "process_medium"
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
|
||||
|
||||
conda (params.conda ? "bioconda::umi_tools=1.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
tuple val(meta), path("*.tsv"), emit: tsv
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
"""
|
||||
umi_tools dedup \\
|
||||
-I $bam \\
|
||||
-S ${prefix}.bam \\
|
||||
--output-stats=$prefix \\
|
||||
$ioptions.args \\
|
||||
|
||||
umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
59
software/umitools/extract/functions.nf
Normal file
59
software/umitools/extract/functions.nf
Normal file
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
54
software/umitools/extract/main.nf
Normal file
54
software/umitools/extract/main.nf
Normal file
|
@ -0,0 +1,54 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
process UMITOOLS_EXTRACT {
|
||||
tag "$meta.id"
|
||||
label "process_low"
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
|
||||
//container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
|
||||
|
||||
conda (params.conda ? "bioconda::umi_tools=1.0.1" : null)
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
val options
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fastq.gz"), emit: reads
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
umi_tools \\
|
||||
extract \\
|
||||
-I $reads \\
|
||||
-S ${prefix}.umi_extract.fastq.gz \\
|
||||
$ioptions.args \\
|
||||
> ${prefix}.umi_extract.log
|
||||
|
||||
umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
umi_tools \\
|
||||
extract \\
|
||||
-I ${reads[0]} \\
|
||||
--read2-in=${reads[1]} \\
|
||||
-S ${prefix}.umi_extract_1.fastq.gz \\
|
||||
--read2-out=${prefix}.umi_extract_2.fastq.gz \\
|
||||
$ioptions.args \\
|
||||
> ${prefix}.umi_extract.log
|
||||
|
||||
umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
}
|
Loading…
Reference in a new issue