mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
682f789f93
* Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
35 lines
1.1 KiB
Text
35 lines
1.1 KiB
Text
process VCFLIB_VCFUNIQ {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1':
|
|
'quay.io/biocontainers/vcflib:1.0.3--hecb563c_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(vcf), path(tbi)
|
|
|
|
output:
|
|
tuple val(meta), path("*.gz"), emit: vcf
|
|
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 = '1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
vcfuniq \\
|
|
$vcf \\
|
|
| bgzip -c $args > ${prefix}.vcf.gz
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
vcflib: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|