process BCFTOOLS_QUERY { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' : 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" input: tuple val(meta), path(vcf), path(index) path(regions) path(targets) path(samples) output: tuple val(meta), path("*.gz") , emit: vcf path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def regions_file = regions ? "--regions-file ${regions}" : "" def targets_file = targets ? "--targets-file ${targets}" : "" def samples_file = samples ? "--samples-file ${samples}" : "" """ bcftools query \\ --output ${prefix}.vcf.gz \\ ${regions_file} \\ ${targets_file} \\ ${samples_file} \\ $args \\ ${vcf} cat <<-END_VERSIONS > versions.yml "${task.process}": bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ }