nf-core_modules/modules/quast/main.nf

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

    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
    """
}