millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-22 10:59:55 +00:00
Code Issues Releases Packages Activity

re add missing switch meta of merged reads to true

Browse source
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
Show stats Download patch file Download diff file Expand all files Collapse all files

13
subworkflows/local/shortread_adapterremoval.nf
View file

@ -38,11 +38,17 @@ workflow SHORTREAD_ADAPTERREMOVAL {
ADAPTERREMOVAL_PAIRED.out.singles_truncated,
ADAPTERREMOVAL_PAIRED.out.paired_truncated
)
.map { meta, reads ->
def meta_new = meta.clone()
meta_new.single_end = true
[meta_new, reads]
}
.groupTuple()
// Paired-end reads cause a nested tuple during grouping.
// We want to present a flat list of files to `CAT_FASTQ`.
.map { meta, fastq -> [meta, fastq.flatten()] }
CAT_FASTQ(ch_concat_fastq)
ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
@ -56,10 +62,13 @@ workflow SHORTREAD_ADAPTERREMOVAL {
ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
)
.map { meta, reads ->
meta.single_end = true
[meta, reads]
def meta_new = meta.clone()
meta_new.single_end = true
[meta_new, reads]
}
.groupTuple()
.map { meta, fastq -> [meta, fastq.flatten()] }
CAT_FASTQ(ch_concat_fastq)