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32 lines
No EOL
966 B
Text
32 lines
No EOL
966 B
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_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:params.options, publish_dir:getSoftwareName(task.process), publish_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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path fasta
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path gtf
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output:
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path "*.index*" , 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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"""
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bowtie-build --threads $task.cpus ${fasta} ${fasta.baseName}.index
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bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
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"""
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} |