2020-09-10 15:45:11 +00:00
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process BWA_MEM {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
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//container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
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conda (params.conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
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input:
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tuple val(meta), path(reads)
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path index
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path fasta
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val options
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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"""
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bwa mem \\
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$ioptions.args \\
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$read_group \\
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-t $task.cpus \\
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$fasta \\
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$reads \\
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| samtools view $ioptions.args2 -@ $task.cpus -bS -o ${prefix}.bam -
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echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
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"""
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}
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