nf-core_modules/modules/bwa/index/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process BWA_INDEX {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
} else {
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container "quay.io/biocontainers/bwa:0.7.17--hed695b0_7"
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}
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input:
path fasta
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output:
path "bwa" , emit: index
path "versions.yml", emit: versions
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script:
"""
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mkdir bwa
bwa \\
index \\
$options.args \\
$fasta \\
-p bwa/${fasta.baseName}
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
END_VERSIONS
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"""
}