mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
37 lines
1.1 KiB
Text
37 lines
1.1 KiB
Text
process BEDTOOLS_INTERSECT {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
|
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(intervals1), path(intervals2)
|
|
val extension
|
|
|
|
output:
|
|
tuple val(meta), path("*.${extension}"), emit: intersect
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
bedtools \\
|
|
intersect \\
|
|
-a $intervals1 \\
|
|
-b $intervals2 \\
|
|
$args \\
|
|
> ${prefix}.${extension}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
|
END_VERSIONS
|
|
"""
|
|
}
|