process TABIX_BGZIPTABIX { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" input: tuple val(meta), path(input) output: tuple val(meta), path("*.gz"), path("*.tbi"), emit: gz_tbi path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ bgzip --threads ${task.cpus} -c $args $input > ${prefix}.gz tabix $args2 ${prefix}.gz cat <<-END_VERSIONS > versions.yml "${task.process}": tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.gz touch ${prefix}.gz.tbi cat <<-END_VERSIONS > versions.yml "${task.process}": tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ }