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47 lines
1.7 KiB
Text
47 lines
1.7 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process BWA_SAMPE {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
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}
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input:
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tuple val(meta), path(reads), path(sai)
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path index
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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 prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def read_group = meta.read_group ? "-r ${meta.read_group}" : ""
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"""
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INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
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bwa sampe \\
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$options.args \\
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$read_group \\
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\$INDEX \\
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$sai \\
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$reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${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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