mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
32 lines
780 B
Text
32 lines
780 B
Text
def MODULE = "bedtools_intersect"
|
|
params.publish_dir = MODULE
|
|
params.publish_results = "default"
|
|
|
|
process INTERSECT_BED {
|
|
tag "$input_file_1-$input_file_2"
|
|
|
|
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_1)
|
|
path (input_file_2)
|
|
val (intersectbed_args)
|
|
|
|
output:
|
|
stdout()
|
|
|
|
script:
|
|
"""
|
|
bedtools intersect -a ${input_file_1} -b ${input_file_2} ${intersectbed_args}
|
|
"""
|
|
}
|
|
|