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129 lines
4.3 KiB
Text
129 lines
4.3 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/modules/adapterremoval/main'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'
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include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main'
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include {
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ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION1;
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ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION2;
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ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION3;
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} from '../../modules/local/ensure_fastq_extension'
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workflow SHORTREAD_ADAPTERREMOVAL {
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take:
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reads // [[meta], [reads]]
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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, [] )
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ADAPTERREMOVAL_PAIRED ( ch_input_for_adapterremoval.paired, [] )
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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_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
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ENSURE_FASTQ_EXTENSION1(
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Channel.empty().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.pair1_truncated,
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ADAPTERREMOVAL_PAIRED.out.pair2_truncated
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)
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.map { meta, reads ->
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meta.single_end = true
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[meta, reads]
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}
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)
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CAT_FASTQ(
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ENSURE_FASTQ_EXTENSION1.out.reads
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.groupTuple()
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)
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ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
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} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
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ENSURE_FASTQ_EXTENSION1(
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Channel.empty().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
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[meta, reads]
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}
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)
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CAT_FASTQ(
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ENSURE_FASTQ_EXTENSION1.out.reads
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.groupTuple()
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)
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ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
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} else {
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ENSURE_FASTQ_EXTENSION1(
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ADAPTERREMOVAL_PAIRED.out.pair1_truncated
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.map { meta, reads ->
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meta.single_end = true
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[meta, reads]
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}
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)
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ENSURE_FASTQ_EXTENSION2(
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ADAPTERREMOVAL_PAIRED.out.pair2_truncated
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.map { meta, reads ->
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meta.single_end = true
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[meta, reads]
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}
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)
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ENSURE_FASTQ_EXTENSION3(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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ch_adapterremoval_reads_prepped = ENSURE_FASTQ_EXTENSION1.out.reads
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.join(ENSURE_FASTQ_EXTENSION2.out.reads)
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.groupTuple()
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.map { meta, pair1, pair2 ->
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meta.single_end = false
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[ meta, [ pair1, pair2 ].flatten() ]
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}
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.mix(ENSURE_FASTQ_EXTENSION3.out.reads)
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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.log.collect{it[1]},
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ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]}
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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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