nf-core_modules/modules/dshbio/splitbed/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process DSHBIO_SPLITBED {
tag "${meta.id}"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::dsh-bio=2.0.5" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.5--hdfd78af_0"
} else {
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container "quay.io/biocontainers/dsh-bio:2.0.5--hdfd78af_0"
}
input:
tuple val(meta), path(bed)
output:
tuple val(meta), path("*.bed.gz"), emit: bed
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
dsh-bio \\
split-bed \\
$options.args \\
-p $prefix \\
-s '.bed.gz' \\
-i $bed
echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt
"""
}