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42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process BOWTIE_ALIGN {
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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:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::bowtie=1.3.0" : null)
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container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
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input:
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tuple val(meta), path(reads)
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path index
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output:
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tuple val(meta), path("*.sam"), emit: sam
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tuple val(meta), path("*.out"), emit: log
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path "bowtie.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 unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : ''
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"""
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INDEX=`find -L ./ -name "*.1.ebwt" | sed 's/.1.ebwt//'`
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bowtie \\
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--threads $task.cpus \\
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$options.args \\
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$INDEX \\
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-q ${reads} \\
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$unaligned \\
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> ${prefix}.sam 2> ${prefix}.out
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bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
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"""
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}
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