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re add missing switch meta of merged reads to true

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This commit is contained in:
James Fellows Yates 2022-04-05 13:55:11 +02:00
parent 98f082d7b6
commit 82aa89ad63
1 changed files with 11 additions and 2 deletions
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13
subworkflows/local/shortread_adapterremoval.nf
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@ -38,11 +38,17 @@ workflow SHORTREAD_ADAPTERREMOVAL {
ADAPTERREMOVAL_PAIRED.out.singles_truncated, ADAPTERREMOVAL_PAIRED.out.singles_truncated,
ADAPTERREMOVAL_PAIRED.out.paired_truncated ADAPTERREMOVAL_PAIRED.out.paired_truncated
) )
.map { meta, reads ->
def meta_new = meta.clone()
meta_new.single_end = true
[meta_new, reads]
}
.groupTuple() .groupTuple()
// Paired-end reads cause a nested tuple during grouping. // Paired-end reads cause a nested tuple during grouping.
// We want to present a flat list of files to `CAT_FASTQ`. // We want to present a flat list of files to `CAT_FASTQ`.
.map { meta, fastq -> [meta, fastq.flatten()] } .map { meta, fastq -> [meta, fastq.flatten()] }
CAT_FASTQ(ch_concat_fastq) CAT_FASTQ(ch_concat_fastq)
ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
@ -56,10 +62,13 @@ workflow SHORTREAD_ADAPTERREMOVAL {
ADAPTERREMOVAL_PAIRED.out.collapsed_truncated ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
) )
.map { meta, reads -> .map { meta, reads ->
meta.single_end = true def meta_new = meta.clone()
[meta, reads] meta_new.single_end = true
[meta_new, reads]
} }
.groupTuple() .groupTuple()
.map { meta, fastq -> [meta, fastq.flatten()] }
CAT_FASTQ(ch_concat_fastq) CAT_FASTQ(ch_concat_fastq)