mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
40 lines
1.3 KiB
Text
40 lines
1.3 KiB
Text
process UCSC_LIFTOVER {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3' :
|
|
'quay.io/biocontainers/ucsc-liftover:377--h0b8a92a_3' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bed)
|
|
path(chain)
|
|
|
|
output:
|
|
tuple val(meta), path("*.lifted.bed") , emit: lifted
|
|
tuple val(meta), path("*.unlifted.bed"), emit: unlifted
|
|
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}"
|
|
def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
liftOver \\
|
|
$args \
|
|
$bed \\
|
|
$chain \\
|
|
${prefix}.lifted.bed \\
|
|
${prefix}.unlifted.bed
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
ucsc: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|