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95 lines
3.3 KiB
Text
95 lines
3.3 KiB
Text
//
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// Process short raw reads with AdapterRemoval
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//
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/adapterremoval/main'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/adapterremoval/main'
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include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main'
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workflow SHORTREAD_ADAPTERREMOVAL {
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take:
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reads // [[meta], [reads]]
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adapterlist // file
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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ch_input_for_adapterremoval = reads
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.branch{
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single: it[0].single_end
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paired: !it[0].single_end
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}
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ADAPTERREMOVAL_SINGLE ( ch_input_for_adapterremoval.single, adapterlist )
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ADAPTERREMOVAL_PAIRED ( ch_input_for_adapterremoval.paired, adapterlist )
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/*
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* Due to the ~slightly~ very ugly output implementation of the current AdapterRemoval2 version, each file
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* has to be exported in a separate channel and we must manually recombine when necessary.
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*/
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if ( params.shortread_qc_mergepairs && params.shortread_qc_includeunmerged ) {
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ch_concat_fastq = Channel.empty()
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.mix(
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ADAPTERREMOVAL_PAIRED.out.collapsed,
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
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ADAPTERREMOVAL_PAIRED.out.singles_truncated,
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ADAPTERREMOVAL_PAIRED.out.paired_truncated
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)
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.map { meta, reads ->
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[meta + [single_end: true], reads]
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}
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.groupTuple()
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// Paired-end reads cause a nested tuple during grouping.
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// We want to present a flat list of files to `CAT_FASTQ`.
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.map { meta, fastq -> [meta, fastq.flatten()] }
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CAT_FASTQ(ch_concat_fastq)
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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} else if ( params.shortread_qc_mergepairs && !params.shortread_qc_includeunmerged ) {
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ch_concat_fastq = Channel.empty()
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.mix(
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ADAPTERREMOVAL_PAIRED.out.collapsed,
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
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)
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.map { meta, reads ->
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[meta + [single_end: true], reads]
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}
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.groupTuple()
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.map { meta, fastq -> [meta, fastq.flatten()] }
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CAT_FASTQ(ch_concat_fastq)
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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} else {
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ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.paired_truncated
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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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}
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
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ch_multiqc_files = ch_multiqc_files.mix(
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ADAPTERREMOVAL_PAIRED.out.settings,
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ADAPTERREMOVAL_SINGLE.out.settings
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)
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emit:
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reads = ch_adapterremoval_reads_prepped // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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