nf-core_modules/software/bcftools/merge/main.nf
2021-02-12 23:16:52 +00:00

37 lines
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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
"""
}