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81 lines
3.1 KiB
Text
81 lines
3.1 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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path fasta
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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('*.summary.txt') , emit: summary_txt
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tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt
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tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4
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tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed
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tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi
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tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed
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tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi
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tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed
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tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi
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tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed
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tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi
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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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def reference = fasta ? "--fasta ${fasta}" : ""
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def interval = bed ? "--by ${bed}" : ""
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if (bed && args.contains("--by")) {
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exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
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}
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if (!bed && args.contains("--thresholds")) {
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exit 1, "'--thresholds' can only be specified in conjunction with '--by'"
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}
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"""
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mosdepth \\
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--threads $task.cpus \\
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$interval \\
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$reference \\
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$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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touch ${prefix}.quantized.bed.gz
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touch ${prefix}.quantized.bed.gz.csi
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touch ${prefix}.thresholds.bed.gz
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touch ${prefix}.thresholds.bed.gz.csi
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cat <<-END_VERSIONS > versions.yml
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"${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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