// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'

params.options = [:]
options        = initOptions(params.options)

process PLASMIDID {
    tag "$meta.id"
    label 'process_medium'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

    conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0'
    } else {
        container 'quay.io/biocontainers/plasmidid:1.6.5--hdfd78af_0'
    }

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

    output:
    tuple val(meta), path("${prefix}/*final_results.html"), emit: html
    tuple val(meta), path("${prefix}/*final_results.tab") , emit: tab
    tuple val(meta), path("${prefix}/images/")            , emit: images
    tuple val(meta), path("${prefix}/logs/")              , emit: logs
    tuple val(meta), path("${prefix}/data/")              , emit: data
    tuple val(meta), path("${prefix}/database/")          , emit: database
    tuple val(meta), path("${prefix}/fasta_files/")       , emit: fasta_files
    tuple val(meta), path("${prefix}/kmer/")              , emit: kmer
    path "versions.yml"                                   , emit: version

    script:
    def software = getSoftwareName(task.process)
    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    """
    plasmidID \\
        -d $fasta \\
        -s $prefix \\
        -c $scaffold \\
        $options.args \\
        -o .

    mv NO_GROUP/$prefix ./$prefix
    cat <<-END_VERSIONS > versions.yml
    ${getProcessName(task.process)}:
        ${getSoftwareName(task.process)}: \$(plasmidID --version 2>&1)
    END_VERSIONS
    """
}