Skip to content

Reformatted .map{ for strict syntax #6

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
YueYvetteHao wants to merge 1 commit into
base: dev
Choose a base branch
from
Open

Reformatted .map{ for strict syntax #6

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 17 additions & 21 deletions subworkflows/local/dedup_umis.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,19 +48,17 @@ workflow DEDUP_UMIS {
BAMTOOLS_SPLIT ( in_bam )
ch_versions = ch_versions.mix(BAMTOOLS_SPLIT.out.versions.first())
ch_split_bam = BAMTOOLS_SPLIT.out.bam
.map{
meta, bam ->
[bam]
.map { meta, bam ->
[bam]
}
.flatten()
.map{
bam ->
def bam_basename = bam.toString().split('/')[-1]
def split_bam_basename = bam_basename.split(/\./)
def new_meta = [
'id': split_bam_basename.take(split_bam_basename.size()-1).join("."),
]
[ new_meta, bam ]
.map { bam ->
def bam_basename = bam.toString().split('/')[-1]
def split_bam_basename = bam_basename.split(/\./)
def new_meta = [
'id': split_bam_basename.take(split_bam_basename.size()-1).join("."),
]
[ new_meta, bam ]
}

} else {
Expand All @@ -81,11 +79,10 @@ workflow DEDUP_UMIS {
in_bam
.join(in_bai)
.combine(GROUP_TRANSCRIPTS.out.grouped_transcripts.flatten())
.map{
meta, bam, bai, region ->
def region_basename = region.toString().split('/')[-1]
def split_region_basename = region_basename.split(/\./)
[['id': meta.id + "." + split_region_basename[0]], bam, bai, region]
.map { meta, bam, bai, region ->
def region_basename = region.toString().split('/')[-1]
def split_region_basename = region_basename.split(/\./)
[['id': meta.id + "." + split_region_basename[0]], bam, bai, region]
}
)
ch_split_bam = SPLIT_BAM.out.split_bam
Expand Down Expand Up @@ -147,11 +144,10 @@ workflow DEDUP_UMIS {
//
SAMTOOLS_MERGE (
ch_dedup_bam
.map{
meta, bam ->
def bam_basename = bam.toString().split('/')[-1]
def split_bam_basename = bam_basename.split(/\./)
def new_meta = [ 'id': split_bam_basename[0] ]
.map { meta, bam ->
def bam_basename = bam.toString().split('/')[-1]
def split_bam_basename = bam_basename.split(/\./)
def new_meta = [ 'id': split_bam_basename[0] ]
[ new_meta, bam ]
}
.groupTuple(),
Expand Down
Loading