process QUAST { label 'process_medium' conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' : 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }" input: path consensus path fasta path gff val use_fasta val use_gff output: path "${prefix}" , emit: results path '*.tsv' , emit: tsv path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: 'quast' def features = use_gff ? "--features $gff" : '' def reference = use_fasta ? "-r $fasta" : '' """ quast.py \\ --output-dir $prefix \\ $reference \\ $features \\ --threads $task.cpus \\ $args \\ ${consensus.join(' ')} ln -s ${prefix}/report.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": quast: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//') END_VERSIONS """ }