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45acc79667
* nf-core create * svdb merge module and test * remove to-do from test.yml * version * update meta.yml * mosdepth update * update md5sums * add stub * add stub * remove svdb * remove merge * Add tests * code linting fix * undo previous commit * revert code linting fix
68 lines
2.3 KiB
Text
68 lines
2.3 KiB
Text
process MOSDEPTH {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' :
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'quay.io/biocontainers/mosdepth:0.3.3--hdfd78af_1'}"
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input:
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tuple val(meta), path(bam), path(bai)
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path bed
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val window_size
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output:
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tuple val(meta), path('*.global.dist.txt') , emit: global_txt
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tuple val(meta), path('*.region.dist.txt') , emit: regions_txt , optional:true
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tuple val(meta), path('*.summary.txt') , emit: summary_txt
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tuple val(meta), path('*.per-base.d4') , emit: d4 , optional:true
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tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed, optional:true
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tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi, optional:true
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tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed , optional:true
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tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi , optional:true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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if (window_size) {
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interval = "--by ${window_size}"
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} else if ( bed ) {
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interval = "--by ${bed}"
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} else {
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interval = ""
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}
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"""
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mosdepth \\
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$interval \\
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$args \\
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$prefix \\
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$bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.global.dist.txt
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touch ${prefix}.region.dist.txt
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touch ${prefix}.summary.txt
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touch ${prefix}.per-base.d4
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touch ${prefix}.per-base.bed.gz
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touch ${prefix}.per-base.bed.gz.csi
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touch ${prefix}.regions.bed.gz
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touch ${prefix}.regions.bed.gz.csi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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