nf-core_modules/modules/agrvate/main.nf

process AGRVATE {
    tag "$meta.id"
    label 'process_low'

    conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' :
        'quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0' }"

    input:
    tuple val(meta), path(fasta)

    output:
    tuple val(meta), path("${fasta.baseName}-results/${fasta.baseName}-summary.tab"), emit: summary
    path "${fasta.baseName}-results"                                                , emit: results_dir
    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}"
    """
    agrvate \\
        $args \\
        -i $fasta

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        agrvate: \$(echo \$(agrvate -v 2>&1) | sed 's/agrvate v//;')
    END_VERSIONS
    """
}