process SVDB_MERGE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0': 'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }" input: tuple val(meta), path(vcfs) val (priority) output: tuple val(meta), path("*_sv_merge.vcf"), emit: vcf 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 input = "" for (int index = 0; index < vcfs.size(); index++) { input += " ${vcfs[index]}:${priority[index]}" } """ svdb \\ --merge \\ $args \\ --priority ${priority.join(',')} \\ --vcf $input \\ > ${prefix}_sv_merge.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_sv_merge.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) END_VERSIONS """ }