nf-core_modules/tools/fastqc/main.nf

nextflow.preview.dsl = 2

process FASTQC {	
    
    // tag "FastQC - $sample_id"

	input:
	    tuple val(name), path(reads)
		val (outputdir)
        // fastqc_args are best passed into the workflow in the following manner:
        // --fastqc_args="--nogroup -a custom_adapter_file.txt"
		val (fastqc_args)
		val (verbose)

	output:
	    tuple val(name), path ("*fastqc*"), emit: all
		path "*.zip",                       emit: report // e.g. for MultiQC later
	
    // container 'quay.io/biocontainers/fastqc:0.11.8--2' 

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

	script:

		if (verbose){
			println ("[MODULE] FASTQC ARGS: " + fastqc_args)
		}

		"""
		module load fastqc
		fastqc $fastqc_args -q -t 2 $reads

        fastqc --version &> fastqc.version.txt
		"""

}