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

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

process HIFIASM {
    //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), publish_id:'') } // publish_id:meta.id) }

    conda (params.enable_conda ? "bioconda::hifiasm=0.14" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/hifiasm:0.14--h8b12597_0"
    } else {
        container "quay.io/biocontainers/hifiasm:0.14--h8b12597_0"
    }

/*     input:
    tuple val(meta), path(reads) */

    output:
/*     tuple val(meta), path("*.html"), emit: html
    tuple val(meta), path("*.zip") , emit: zip */
    path  "*.version.txt"          , emit: version

    script:
    // Add soft-links to original FastQs for consistent naming in pipeline
    def software = getSoftwareName(task.process)
    //def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"

/*     if (meta.single_end) {
        """
        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
        fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
        """
    } else {
        """
        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
        fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
        """
    } */

    """
    hifiasm --version > ${software}.version.txt || exit 0
    """
}