mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
37 lines
1.3 KiB
Text
37 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process BCFTOOLS_MERGE {
|
|
tag "$meta.id"
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
|
|
|
conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
|
|
} else {
|
|
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(vcfs), path(tbis)
|
|
|
|
output:
|
|
tuple val(meta), path("*.gz"), emit: vcf
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
bcftools merge -Oz \\
|
|
--output ${prefix}.vcf.gz \\
|
|
$options.args \\
|
|
*.vcf.gz
|
|
echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|