//
// Read QC, UMI extraction and trimming
//

include { FASTQC           } from '../../../modules/nf-core/fastqc/main'
include { UMITOOLS_EXTRACT } from '../../../modules/nf-core/umitools/extract/main'
include { TRIMGALORE       } from '../../../modules/nf-core/trimgalore/main'

//
// Function that parses TrimGalore log output file to get total number of reads after trimming
//
def getTrimGaloreReadsAfterFiltering(log_file) {
    def total_reads = 0
    def filtered_reads = 0
    log_file.eachLine { line ->
        def total_reads_matcher = line =~ /([\d\.]+)\ssequences processed in total/
        def filtered_reads_matcher = line =~ /shorter than the length cutoff[^:]+:\s([\d\.]+)/
        if (total_reads_matcher) total_reads = total_reads_matcher[0][1].toFloat()
        if (filtered_reads_matcher) filtered_reads = filtered_reads_matcher[0][1].toFloat()
    }
    return total_reads - filtered_reads
}

workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE {
    take:
    reads            // channel: [ val(meta), [ reads ] ]
    skip_fastqc      // boolean: true/false
    with_umi         // boolean: true/false
    skip_umi_extract // boolean: true/false
    skip_trimming    // boolean: true/false
    umi_discard_read // integer: 0, 1 or 2

    main:

    ch_versions = Channel.empty()
    fastqc_html = Channel.empty()
    fastqc_zip  = Channel.empty()
    if (!skip_fastqc) {
        FASTQC ( reads ).html.set { fastqc_html }
        fastqc_zip  = FASTQC.out.zip
        ch_versions = ch_versions.mix(FASTQC.out.versions.first())
    }

    umi_reads = reads
    umi_log   = Channel.empty()
    if (with_umi && !skip_umi_extract) {

            UMITOOLS_EXTRACT ( reads ).reads.set { umi_reads }
            umi_log     = UMITOOLS_EXTRACT.out.log
            ch_versions = ch_versions.mix(UMITOOLS_EXTRACT.out.versions.first())

            // Discard R1 / R2 if required
            if (umi_discard_read in [1,2]) {
                UMITOOLS_EXTRACT
                    .out
                    .reads
                    .map { meta, reads ->
                        if (!meta.single_end) {
                            meta['single_end'] = true
                            reads = reads[umi_discard_read % 2]
                        }
                        return [ meta, reads ]
                    }
                    .set { umi_reads }
            }
    }

    trim_reads    = umi_reads
    trim_unpaired = Channel.empty()
    trim_html     = Channel.empty()
    trim_zip      = Channel.empty()
    trim_log      = Channel.empty()
    if (!skip_trimming) {
        TRIMGALORE ( umi_reads ).reads.set { trim_reads }
        trim_unpaired = TRIMGALORE.out.unpaired
        trim_html     = TRIMGALORE.out.html
        trim_zip      = TRIMGALORE.out.zip
        trim_log      = TRIMGALORE.out.log
        ch_versions   = ch_versions.mix(TRIMGALORE.out.versions.first())

        //
        // Filter empty FastQ files after adapter trimming
        //
        trim_reads
            .join(trim_log)
            .map {
                meta, reads, trim_log ->
                    if (!meta.single_end) {
                        trim_log = trim_log[-1]
                    }
                    if (getTrimGaloreReadsAfterFiltering(trim_log) > 0) {
                        [ meta, reads ]
                    }
            }
            .set { trim_reads }
    }

    emit:
    reads = trim_reads // channel: [ val(meta), [ reads ] ]

    fastqc_html        // channel: [ val(meta), [ html ] ]
    fastqc_zip         // channel: [ val(meta), [ zip ] ]

    umi_log            // channel: [ val(meta), [ log ] ]

    trim_unpaired      // channel: [ val(meta), [ reads ] ]
    trim_html          // channel: [ val(meta), [ html ] ]
    trim_zip           // channel: [ val(meta), [ zip ] ]
    trim_log           // channel: [ val(meta), [ txt ] ]

    versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
}
