nf-core_modules/software/bedtools/merge/main.nf

32 lines
882 B
Text

def MODULE = "bedtools_merge"
params.publish_dir = MODULE
params.publish_results = "default"
process BEDTOOLS_MERGE {
tag { input_file }
publishDir "${params.out_dir}/${params.publish_dir}",
mode: params.publish_dir_mode,
saveAs: { filename ->
if (params.publish_results == "none") null
else filename }
//container "docker.pkg.github.com/nf-core/$MODULE"
container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
conda "${moduleDir}/environment.yml"
input:
path (input_file)
val (bedtools_merge_args)
output:
path "${input_file}.bed", emit: merge
path "*.version.txt", emit: version
script:
"""
bedtools merge -i ${input_file} ${bedtools_merge_args} > ${input_file}.bed
bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
"""
}