process VARIANTBAM { tag "$meta.id" label 'process_medium' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5' : 'quay.io/biocontainers/variantbam:1.4.4a--h7d7f7ad_5' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.bam"), emit: bam 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}" def VERSION = '1.4.4a' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ variant \\ $bam \\ -o ${prefix}.bam \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": variantbam: $VERSION END_VERSIONS """ }