nf-core_modules/modules/bedtools/makewindows/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BEDTOOLS_MAKEWINDOWS {
tag "$meta.id"
label 'process_low'
publishDir "${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']) }
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1"
} else {
container "quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1"
}
input:
tuple val(meta), path(regions)
val(use_bed)
output:
tuple val(meta), path("*.tab"), emit: tab
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def arg_input = use_bed ? "-b $regions" : "-g $regions"
"""
bedtools \\
makewindows \\
${arg_input} \\
$options.args \\
> ${prefix}.tab
echo \$(bedtools --version) | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}