nf-core_modules/modules/bwameth/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 BWAMETH_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::bwameth=0.2.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1"
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} else {
container "quay.io/biocontainers/bwameth:0.2.2--py_1"
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}
input:
path fasta, stageAs: "bwameth/*"
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output:
path "bwameth" , emit: index
path "versions.yml" , emit: versions
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script:
"""
bwameth.py index $fasta
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(bwameth.py --version 2>&1) | cut -f2 -d" ")
END_VERSIONS
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"""
}