nf-core_modules/modules/ucsc/liftover/main.nf
Benjamin Wingfield 4ed5e4eff3
New module: ucsc/liftover (#868)
* add liftOver module

* add liftover module tests

* fix getProcessName

* fix tests

* fix out of date function

* version numbers should be numeric

* drop versions.yml from test.yml

* Update modules/ucsc/liftover/main.nf

Remove software name variable

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update tests/modules/ucsc/liftover/main.nf

Use test chain file

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* add genome_chain_gz to test data config

* update md5sum for new chain test data

* Fix indentation in file declaration

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-10-21 18:04:15 +02:00

48 lines
1.5 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
def VERSION = '377'
process UCSC_LIFTOVER {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3"
} else {
container "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
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
liftOver \\
$options.args \
$bed \\
$chain \\
${prefix}.lifted.bed \\
${prefix}.unlifted.bed
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo "$VERSION")
END_VERSIONS
"""
}