process DELLY_CALL { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::delly=1.1.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/delly:1.1.3--h358d541_0' : 'quay.io/biocontainers/delly:1.1.3--h358d541_0' }" input: tuple val(meta), path(bam), path(bai) path fasta path fai output: tuple val(meta), path("*.bcf"), emit: bcf tuple val(meta), path("*.csi"), emit: csi 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}" """ delly \\ call \\ $args \\ -o ${prefix}.bcf \\ -g $fasta \\ $bam \\ cat <<-END_VERSIONS > versions.yml "${task.process}": delly: \$( echo \$(delly --version 2>&1) | sed 's/^.*Delly version: v//; s/ using.*\$//') END_VERSIONS """ }