process SVDB_QUERY { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0': 'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }" input: tuple val(meta), path(vcf) val(in_occs) val(in_frqs) val(out_occs) val(out_frqs) path (vcf_dbs) output: tuple val(meta), path("*_query.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 in_occ = "" def in_frq = "" def out_occ = "" def out_frq = "" if (in_occs) { in_occ = "--in_occ ${in_occs.join(',')}" } if (in_frqs) { in_frq = "--in_frq ${in_frqs.join(',')}" } if (out_occs) { out_occ = "--out_occ ${out_occs.join(',')}" } if (out_frqs) { out_frq = "--out_frq ${out_frqs.join(',')}" } """ svdb \\ --query \\ $in_occ \\ $in_frq \\ $out_occ \\ $out_frq \\ $args \\ --db ${vcf_dbs.join(',')} \\ --query_vcf $vcf \\ --prefix ${prefix} cat <<-END_VERSIONS > versions.yml "${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 ${prefix}_query.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) END_VERSIONS """ }