nf-core_modules/software/bowtie/build/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process BOWTIE_BUILD {
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tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
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conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1'
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} else {
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container 'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1'
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}
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input:
path fasta
output:
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path 'bowtie' , 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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mkdir bowtie
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bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
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"""
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}