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40 lines
1.1 KiB
Text
40 lines
1.1 KiB
Text
process DEDUP {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/dedup:0.12.8--hdfd78af_1' :
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'quay.io/biocontainers/dedup:0.12.8--hdfd78af_1' }"
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*_rmdup.bam"), emit: bam // _rmdup is hardcoded output from dedup
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tuple val(meta), path("*.json") , emit: json
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tuple val(meta), path("*.hist") , emit: hist
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tuple val(meta), path("*log") , emit: log
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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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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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dedup \\
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-Xmx${task.memory.toGiga()}g \\
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-i $bam \\
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-o . \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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dedup: \$( echo \$(dedup --version 2>&1) | tail -n 1 | sed 's/.* v//')
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END_VERSIONS
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"""
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}
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