process BCFTOOLS_MERGE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" input: tuple val(meta), path(vcfs), path(tbis) output: tuple val(meta), path("*.gz"), emit: vcf path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ bcftools merge -Oz \\ --output ${prefix}.vcf.gz \\ $args \\ *.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ }