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https://github.com/MillironX/nf-core_modules.git
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Apply suggestions from code review
Add all initial suggestions from review (syntax issues) Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
sruthipsuresh
sruthipsuresh
parent
e5c21d15a3
commit
fc8cdde2b4
6 changed files with 41 additions and 29 deletions
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@ -32,7 +32,7 @@ input:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bed:
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- beds:
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type: file
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description: List of bed files
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pattern: "*.{bed}"
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@ -46,7 +46,6 @@ output:
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type: file
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description: Edited bed file
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pattern: "*.{complement.bed}"
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- version:
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type: file
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description: File containing software version
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@ -1,6 +1,7 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process BEDTOOLS_GENOMECOV {
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@ -10,11 +11,11 @@ process BEDTOOLS_GENOMECOV {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
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container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
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} else {
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container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
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container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
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}
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input:
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@ -29,6 +30,6 @@ process BEDTOOLS_GENOMECOV {
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools genomecov -ibam $bams -g $sizes ${options.args} > ${prefix}.bed
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bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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}
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@ -1,6 +1,7 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process BEDTOOLS_INTERSECT {
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@ -10,24 +11,31 @@ process BEDTOOLS_INTERSECT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
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container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
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} else {
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container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
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container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
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}
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input:
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tuple val(meta), path(bedfile1), path(bedfile2)
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tuple val(meta), path(bed1), path(bed2)
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output:
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tuple val(meta), path("*.intersect.bed"), emit: intersect
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tuple val(meta), path("*.intersect.bed"), emit: bed
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path "*.version.txt", emit: version
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script: // TODO change script to account for multiple possible intersections
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools intersect -a ${bedfile1} -b ${bedfile2} ${options.args} > ${prefix}.intersect.bed
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bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
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bedtools \\
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intersect \\
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-a ${bed1} \\
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-b ${bed2} \\
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$options.args \\
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> ${prefix}.intersect.bed
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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}
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@ -1,6 +1,7 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process BEDTOOLS_MERGE {
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@ -10,23 +11,24 @@ process BEDTOOLS_MERGE {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
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container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
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} else {
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container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
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container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
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}
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input:
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tuple val(meta), path(sort)
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tuple val(meta), path(bed)
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output:
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path("*.merged.bed"), emit: merge
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path("*.merged.bed"), emit: bed
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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 prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools merge -i ${sort} ${options.args} > ${prefix}.merged.bed
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bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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}
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@ -1,5 +1,6 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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@ -10,11 +11,11 @@ process BEDTOOLS_SLOP {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
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container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
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} else {
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container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
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container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
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}
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@ -22,7 +23,7 @@ process BEDTOOLS_SLOP {
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tuple val(meta), path(beds), path (sizes)
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output:
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tuple val(meta), path("*.slop.bed"), emit: slopbed
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tuple val(meta), path("*.slop.bed"), emit: bed
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path "*.version.txt", emit: version
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script:
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@ -41,7 +42,7 @@ process BEDTOOLS_SLOP {
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} else {
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"""
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slopBed -i $beds -g $sizes -l $params.l -r $params.r $header $pct $options.args> ${prefix}.slop.bed
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bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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}
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}
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@ -1,6 +1,7 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process BEDTOOLS_SORT {
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@ -10,18 +11,18 @@ process BEDTOOLS_SORT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
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container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
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} else {
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container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
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container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
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}
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input:
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tuple val(meta), path(beds)
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output:
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tuple val(meta), path("*.sort.bed"), emit: sort
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tuple val(meta), path("*.sort.bed"), emit: bed
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path "*.version.txt", emit: version
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script:
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@ -29,6 +30,6 @@ process BEDTOOLS_SORT {
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools sort -i $beds ${options.args} > ${prefix}.sort.bed
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bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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}
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