nf-core_modules/software/bedtools/merge/main.nf
2021-01-29 23:17:44 -06:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
def options = initOptions(params.options)
process BEDTOOLS_MERGE {
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), publish_id:'') }
conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
} else {
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
}
input:
tuple val(meta), path(sort)
output:
path("*.merged.bed"), emit: merge
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
bedtools merge -i ${sort} ${options.args} > ${prefix}.merged.bed
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
"""
}