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f0a86eaf5b
* Multithreaded samtools commands * Updated the checksums since the BAM files include the actual command line Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
process SAMTOOLS_AMPLICONCLIP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
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'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
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input:
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tuple val(meta), path(bam)
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path bed
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val save_cliprejects
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val save_clipstats
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.clipstats.txt") , optional:true, emit: stats
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tuple val(meta), path("*.cliprejects.bam"), optional:true, emit: rejects_bam
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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 rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
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def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : ""
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if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
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"""
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samtools \\
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ampliconclip \\
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--threads ${task.cpus-1} \\
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$args \\
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$rejects \\
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$stats \\
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-b $bed \\
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-o ${prefix}.bam \\
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$bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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