nf-core_modules/modules/artic/minion/main.nf

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

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

process ARTIC_MINION {
    tag "$meta.id"
    label 'process_high'
    publishDir "${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::artic=1.2.1" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
    } else {
        container "quay.io/biocontainers/artic:1.2.1--py_0"
    }

    input:
    tuple val(meta), path(fastq)
    path  fast5_dir
    path  sequencing_summary
    path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
    path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
    path  medaka_model
    val   scheme
    val   scheme_version

    output:
    tuple val(meta), path("${prefix}.*")                              , emit: results
    tuple val(meta), path("${prefix}.sorted.bam")                     , emit: bam
    tuple val(meta), path("${prefix}.sorted.bam.bai")                 , emit: bai
    tuple val(meta), path("${prefix}.trimmed.rg.sorted.bam")          , emit: bam_trimmed
    tuple val(meta), path("${prefix}.trimmed.rg.sorted.bam.bai")      , emit: bai_trimmed
    tuple val(meta), path("${prefix}.primertrimmed.rg.sorted.bam")    , emit: bam_primertrimmed
    tuple val(meta), path("${prefix}.primertrimmed.rg.sorted.bam.bai"), emit: bai_primertrimmed
    tuple val(meta), path("${prefix}.consensus.fasta")                , emit: fasta
    tuple val(meta), path("${prefix}.pass.vcf.gz")                    , emit: vcf
    tuple val(meta), path("${prefix}.pass.vcf.gz.tbi")                , emit: tbi
    tuple val(meta), path("*.json"), optional:true                    , emit: json
    path  "versions.yml"                                              , emit: versions

    script:
    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    def version  = scheme_version.toString().toLowerCase().replaceAll('v','')
    def fast5    = params.fast5_dir          ? "--fast5-directory $fast5_dir"             : ""
    def summary  = params.sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
    def model    = ""
    if (options.args.tokenize().contains('--medaka')) {
        fast5   = ""
        summary = ""
        model = file(params.artic_minion_medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $params.artic_minion_medaka_model"
    }
    """
    artic \\
        minion \\
        $options.args \\
        --threads $task.cpus \\
        --read-file $fastq \\
        --scheme-directory ./primer-schemes \\
        --scheme-version $version \\
        $model \\
        $fast5 \\
        $summary \\
        $scheme \\
        $prefix

    cat <<-END_VERSIONS > versions.yml
    ${getProcessName(task.process)}:
        ${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
    END_VERSIONS
    """
}