mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2025-01-08 15:02:09 -05:00
36 lines
1.4 KiB
Text
36 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process BEDTOOLS_ERNAS {
|
|
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:meta.id) }
|
|
|
|
conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.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(nogenesbed)
|
|
path "H3K27ac"
|
|
path "H3K4me1"
|
|
|
|
output:
|
|
tuple val(meta), path("*.erna.bed"), emit: ernabed
|
|
path "*.version.txt", emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
bedtools intersect -a $nogenesbed -b $nogenesbed $H3K27ac $H3K4me1 -sorted -u -bed > ${prefix}.erna.bed
|
|
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
|
|
"""
|
|
}
|