process TIDDIT_SV { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' : 'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }" input: tuple val(meta), path(bam) path fasta path fai output: tuple val(meta), path("*.vcf") , emit: vcf tuple val(meta), path("*.ploidy.tab") , emit: ploidy tuple val(meta), path("*.signals.tab"), emit: signals path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : "" """ tiddit \\ --sv \\ $args \\ --bam $bam \\ $reference \\ -o $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') END_VERSIONS """ }