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31 lines
947 B
Text
31 lines
947 B
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process BWA_INDEX {
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tag "$fasta"
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label 'process_high'
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publishDir "${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:'') }
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container "biocontainers/bwa:v0.7.17_cv1"
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//container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
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conda (params.conda ? "bioconda::bwa=0.7.17" : null)
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input:
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path fasta
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val options
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output:
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path "${fasta}.*", emit: index
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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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"""
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bwa index $ioptions.args $fasta
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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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