mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 10:09:55 +00:00
129 lines
4.3 KiB
Text
129 lines
4.3 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'
|
|
include {
|
|
ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION1;
|
|
ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION2;
|
|
ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION3;
|
|
} from '../../modules/local/ensure_fastq_extension'
|
|
|
|
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~ very 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 ) {
|
|
|
|
ENSURE_FASTQ_EXTENSION1(
|
|
Channel.empty().mix(
|
|
ADAPTERREMOVAL_PAIRED.out.collapsed,
|
|
ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
|
|
ADAPTERREMOVAL_PAIRED.out.singles_truncated,
|
|
ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
|
|
ADAPTERREMOVAL_PAIRED.out.pair2_truncated
|
|
)
|
|
.map { meta, reads ->
|
|
meta.single_end = true
|
|
[meta, reads]
|
|
}
|
|
)
|
|
|
|
CAT_FASTQ(
|
|
ENSURE_FASTQ_EXTENSION1.out.reads
|
|
.groupTuple()
|
|
)
|
|
|
|
ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
|
|
|
|
ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
|
|
.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
|
|
|
|
} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
|
|
|
|
ENSURE_FASTQ_EXTENSION1(
|
|
Channel.empty().mix(
|
|
ADAPTERREMOVAL_PAIRED.out.collapsed,
|
|
ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
|
|
)
|
|
.map { meta, reads ->
|
|
meta.single_end = true
|
|
[meta, reads]
|
|
}
|
|
)
|
|
|
|
CAT_FASTQ(
|
|
ENSURE_FASTQ_EXTENSION1.out.reads
|
|
.groupTuple()
|
|
)
|
|
|
|
ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
|
|
|
|
ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
|
|
.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
|
|
|
|
} else {
|
|
|
|
ENSURE_FASTQ_EXTENSION1(
|
|
ADAPTERREMOVAL_PAIRED.out.pair1_truncated
|
|
.map { meta, reads ->
|
|
meta.single_end = true
|
|
[meta, reads]
|
|
}
|
|
)
|
|
|
|
ENSURE_FASTQ_EXTENSION2(
|
|
ADAPTERREMOVAL_PAIRED.out.pair2_truncated
|
|
.map { meta, reads ->
|
|
meta.single_end = true
|
|
[meta, reads]
|
|
}
|
|
)
|
|
|
|
ENSURE_FASTQ_EXTENSION3(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
|
|
|
|
ch_adapterremoval_reads_prepped = ENSURE_FASTQ_EXTENSION1.out.reads
|
|
.join(ENSURE_FASTQ_EXTENSION2.out.reads)
|
|
.groupTuple()
|
|
.map { meta, pair1, pair2 ->
|
|
meta.single_end = false
|
|
[ meta, [ pair1, pair2 ].flatten() ]
|
|
}
|
|
.mix(ENSURE_FASTQ_EXTENSION3.out.reads)
|
|
|
|
}
|
|
|
|
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_adapterremoval_reads_prepped // channel: [ val(meta), [ reads ] ]
|
|
versions = ch_versions // channel: [ versions.yml ]
|
|
mqc = ch_multiqc_files
|
|
}
|
|
|