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refactor: remove superfluous ENSURE_FASTQ_EXTENSION

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This commit is contained in:
Moritz E. Beber 2022-04-05 10:53:04 +02:00
parent c54c32c494
commit 0e9b2989e3
1 changed files with 16 additions and 59 deletions
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75
subworkflows/local/shortread_adapterremoval.nf
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@ -5,11 +5,6 @@ Process short raw reads with AdapterRemoval
include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main' 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 { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'
include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/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 { workflow SHORTREAD_ADAPTERREMOVAL {
@ -36,34 +31,25 @@ workflow SHORTREAD_ADAPTERREMOVAL {
if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) { if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
ENSURE_FASTQ_EXTENSION1( ch_concat_fastq = Channel.empty()
Channel.empty().mix( .mix(
ADAPTERREMOVAL_PAIRED.out.collapsed, ADAPTERREMOVAL_PAIRED.out.collapsed,
ADAPTERREMOVAL_PAIRED.out.collapsed_truncated, ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
ADAPTERREMOVAL_PAIRED.out.singles_truncated, ADAPTERREMOVAL_PAIRED.out.singles_truncated,
ADAPTERREMOVAL_PAIRED.out.pair1_truncated, ADAPTERREMOVAL_PAIRED.out.paired_truncated
ADAPTERREMOVAL_PAIRED.out.pair2_truncated
) )
.map { meta, reads -> .groupTuple()
meta.single_end = true .map { [it.head(), it.tail().flatten()] }
[meta, reads]
}
)
CAT_FASTQ( CAT_FASTQ(ch_concat_fastq)
ENSURE_FASTQ_EXTENSION1.out.reads
.groupTuple()
)
ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
.mix(ENSURE_FASTQ_EXTENSION2.out.reads) .mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) { } else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
ENSURE_FASTQ_EXTENSION1( ch_concat_fastq = Channel.empty()
Channel.empty().mix( .mix(
ADAPTERREMOVAL_PAIRED.out.collapsed, ADAPTERREMOVAL_PAIRED.out.collapsed,
ADAPTERREMOVAL_PAIRED.out.collapsed_truncated ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
) )
@ -71,54 +57,25 @@ workflow SHORTREAD_ADAPTERREMOVAL {
meta.single_end = true meta.single_end = true
[meta, reads] [meta, reads]
} }
) .groupTuple()
CAT_FASTQ( CAT_FASTQ(ch_concat_fastq)
ENSURE_FASTQ_EXTENSION1.out.reads
.groupTuple()
)
ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
.mix(ENSURE_FASTQ_EXTENSION2.out.reads) .mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
} else { } else {
ENSURE_FASTQ_EXTENSION1( ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.paired_truncated
ADAPTERREMOVAL_PAIRED.out.pair1_truncated .mix(ADAPTERREMOVAL_SINGLE.out.singles_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_SINGLE.out.versions.first() )
ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() ) ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
ch_multiqc_files = ch_multiqc_files.mix( ch_multiqc_files = ch_multiqc_files.mix(
ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]}, ADAPTERREMOVAL_PAIRED.out.settings.collect{it[1]},
ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]} ADAPTERREMOVAL_SINGLE.out.settings.collect{it[1]}
) )
emit: emit: