nf-core_modules/modules/bedtools/merge/main.nf
2022-02-04 09:53:32 +01:00

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process BEDTOOLS_MERGE {
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(bed)
output:
tuple val(meta), path('*.bed'), emit: bed
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 \\
merge \\
-i $bed \\
$args \\
> ${prefix}.bed
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
}