nf-core_modules/modules/mash/screen/main.nf

process MASH_SCREEN {
    tag "$meta.id"
    label 'process_medium'

    conda (params.enable_conda ? "bioconda::mash=2.3" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1':
        'quay.io/biocontainers/mash:2.3--he348c14_1' }"

    input:
    tuple val(meta), path(query_sketch)
    path fastx_db

    output:
    tuple val(meta), path("*.screen"), emit: screen
    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}"
    """
    mash \\
        screen \\
        $args \\
        -p $task.cpus \\
        $query_sketch \\
        $fastx_db \\
        > ${prefix}.screen

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        mash: \$( mash --version )
    END_VERSIONS
    """
}