nf-core_modules/software/fastq_screen/main.nf

nextflow.preview.dsl=2

process FASTQ_SCREEN {

    // depending on the number of genomes and the type of genome (e.g. plants!), memory needs to be ample!
    // label 'bigMem'
    // label 'multiCore'

    input:
        tuple val(name), path(reads)
        val (outputdir)
        // fastq_screen_args are best passed in to the workflow in the following manner:
        // --fastq_screen_args="--subset 200000 --force"
        val (fastq_screen_args)
        val (verbose)

    output:
        path "*png",  emit: png
        path "*html", emit: html
        path "*txt",  emit: report

    publishDir "$outputdir",
        mode: "link", overwrite: true

    script:
        println(name)
        println(reads)
        println(outputdir)
        if (verbose){
            println ("[MODULE] FASTQ SCREEN ARGS: "+ fastq_screen_args)
        }

    """
    module load fastq_screen
    fastq_screen $fastq_screen_args $reads
    """

}