#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { FASTQC                      } from '../../../../modules/fastqc/main.nf'                      addParams( options: [:]                    )
include { MULTIQC                     } from '../../../../modules/multiqc/main.nf'                     addParams( options: [:]                    )
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/custom/dumpsoftwareversions/main.nf' addParams( options: [publish_dir:'custom'] )

workflow test_custom_dumpsoftwareversions {
    input = [
        [ id: 'test', single_end: false ],
        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
    ]

    FASTQC  ( input )
    MULTIQC ( FASTQC.out.zip.collect { it[1] } )

    ch_software_versions = Channel.empty()
    ch_software_versions = ch_software_versions.mix(FASTQC.out.versions)
    ch_software_versions = ch_software_versions.mix(MULTIQC.out.versions)

    CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
}