taxprofiler/subworkflows/local/shortread_adapterremoval.nf

/*
Process short raw reads with AdapterRemoval
*/

include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE       } from '../../modules/nf-core/modules/adapterremoval/main'
include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED       } from '../../modules/nf-core/modules/adapterremoval/main'
include { CAT_FASTQ                                     } from '../../modules/nf-core/modules/cat/fastq/main'

workflow SHORTREAD_ADAPTERREMOVAL {

    take:
    reads // [[meta], [reads]]

    main:
    ch_versions = Channel.empty()
    ch_multiqc_files      = Channel.empty()

    ch_input_for_adapterremoval = reads
                                    .branch{
                                        single: it[0].single_end
                                        paired: !it[0].single_end
                                    }

    ADAPTERREMOVAL_SINGLE ( ch_input_for_adapterremoval.single, [] )
    ADAPTERREMOVAL_PAIRED ( ch_input_for_adapterremoval.paired, [] )

    // due to the slightly ugly output implementation of the current AdapterRemoval2 version, each file
    // has to be exported in a separate channel, and we must manually recombine when necessary

    if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
        ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
                                                .mix(
                                                    ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
                                                    ADAPTERREMOVAL_PAIRED.out.singles_truncated,
                                                    ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
                                                    ADAPTERREMOVAL_PAIRED.out.pair2_truncated
                                                    )
                                                .map {
                                                    meta, reads ->
                                                        def meta_new = meta.clone()
                                                        meta_new.single_end = true

                                                        [ meta_new, reads ]
                                                    }
                                                    .groupTuple()

        ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
                                            .mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )

    } else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
        ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
                                                .mix( ADAPTERREMOVAL_PAIRED.out.collapsed_truncated )
                                                .map {
                                                    meta, reads ->
                                                        def meta_new = meta.clone()
                                                        meta_new['single_end'] = true

                                                        [ meta_new, reads ]
                                                    }
                                                    .groupTuple(by: 0)

        ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
                                            .mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )

    } else {

        ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.pair1_truncated
                                                .join( ADAPTERREMOVAL_PAIRED.out.pair2_truncated )
                                                .groupTuple()
                                                .map { meta, pair1, pair2 ->
                                                        [ meta, [ pair1, pair2 ].flatten() ]
                                                }
                                            .mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
    }

    ch_processed_reads = ch_adapterremoval_reads_prepped

    ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
    ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
    ch_multiqc_files = ch_multiqc_files.mix( ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]}, ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]} )

    emit:
    reads    = ch_processed_reads   // channel: [ val(meta), [ reads ] ]
    versions = ch_versions          // channel: [ versions.yml ]
    mqc      = ch_multiqc_files
}