process BCFTOOLS_CONSENSUS { 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(tbi), path(fasta) output: tuple val(meta), path('*.fa'), emit: fasta 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}" """ cat $fasta \\ | bcftools \\ consensus \\ $vcf \\ $args \\ > ${prefix}.fa cat <<-END_VERSIONS > versions.yml "${task.process}": bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ }