mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-24 17:49:54 +00:00
86 lines
4.5 KiB
Text
86 lines
4.5 KiB
Text
//
|
|
// 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
|
|
}
|