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

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def VERSION = '377' // Version information not provided by tool on CLI
process UCSC_LIFTOVER {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null)
container "${ 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}"
"""
liftOver \\
$args \
$bed \\
$chain \\
${prefix}.lifted.bed \\
${prefix}.unlifted.bed
cat <<-END_VERSIONS > versions.yml
"${task.process}":
ucsc: $VERSION
END_VERSIONS
"""
}