mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
34 lines
1.1 KiB
Text
34 lines
1.1 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process BEDTOOLS_BAMTOBED {
|
|
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']) }
|
|
|
|
conda (params.enable_conda ? "bioconda::bedtools=2.29.2" : null)
|
|
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
|
|
|
|
input:
|
|
tuple val(meta), path(sizes), path(bam), path(bai)
|
|
|
|
output:
|
|
tuple val(meta), path(sizes), path("*.bed12"), emit: bed12
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
"""
|
|
bedtools \\
|
|
bamtobed \\
|
|
-bed12 \\
|
|
-cigar \\
|
|
-i ${bam[0]} \\
|
|
| bedtools sort > ${meta.id}.bed12
|
|
bedtools --version | sed -e "s/bedtools v//g" > bedtools.version.txt
|
|
"""
|
|
}
|