nf-core_modules/tools/multiqc/main.nf

nextflow.preview.dsl=2

process MULTIQC {
	
    // tag "FastQC - $sample_id"
    
    input:
	    path (file)
		val (outdir)
		val (multiqc_args)
        // multiqc_args are best passed into the workflow in the following manner:
        // --multiqc_args="--exlude STAR --title custom_report_title"
		val (verbose)

	output:
	    path "*html",       emit: html

	publishDir "${outdir}/multiqc",
		mode: "copy", overwrite: true

    script:

		if (verbose){
			println ("[MODULE] MULTIQC ARGS: " + multiqc_args)
		}

		"""
		multiqc $multiqc_args -x work . 
		"""

}