nf-core_modules/modules/cooler/digest/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process COOLER_DIGEST {
tag "$fasta"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0"
} else {
container "quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0"
}
input:
path fasta
path chromsizes
val enzyme
output:
path "*.bed" , emit: bed
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
"""
cooler digest \\
$options.args \\
-o "${fasta.baseName}_${enzyme.replaceAll(/[^0-9a-zA-Z]+/, '_')}.bed" \\
$chromsizes \\
$fasta \\
$enzyme
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(cooler --version 2>&1 | sed 's/cooler, version //')
END_VERSIONS
"""
}