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6806cd1de9
* feat(bbmap): Initialize pileup module * test(bbmap): Update outputs * test(bbmap): Add pileup tags * style(bbmap): Add in when Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
39 lines
1.4 KiB
Text
39 lines
1.4 KiB
Text
process BBMAP_PILEUP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
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'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
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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("*.stats.txt"), emit: covstats
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tuple val(meta), path("*.hist.txt") , emit: hist
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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 ?: "${meta.id}"
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"""
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pileup.sh \\
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-Xmx${task.memory.toGiga()}g \\
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in=${bam} \\
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out=${prefix}.coverage.stats.txt \\
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hist=${prefix}.coverage.hist.txt \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bbmap: \$(bbversion.sh)
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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