process SCOARY { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2' : 'quay.io/biocontainers/scoary:1.6.16--py_2' }" input: tuple val(meta), path(genes), path(traits) path(tree) output: tuple val(meta), path("*.csv"), emit: csv path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def newick_tree = tree ? "-n ${tree}" : "" """ scoary \\ $args \\ --no-time \\ --threads $task.cpus \\ --traits $traits \\ --genes $genes cat <<-END_VERSIONS > versions.yml "${task.process}": scoary: \$( scoary --version 2>&1 ) END_VERSIONS """ }