Skip to content

fix issue when sex field in samplesheet is empty #118

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

Merged
nvnieuwk merged 1 commit into from
Sep 17, 2025
Merged

fix issue when sex field in samplesheet is empty #118

Show file tree
Hide file tree
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
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
1. Fail the pipeline when the sex determination failed. This will now prompt the user to add the sex to the samplesheet so the pipeline doesn't do any wrong assumptions
2. Fixed the Jasmine module output VCFs being empty when no variants have been merged. This file now contains the header of one of the input VCFs
3. AnnotSV VCF files are now sorted before trying to combine it with the VEP output.
4. Fixed a map issue when the sex field is empty in the samplesheet

## v0.2.0 - [19 July 2024] - Mighty Manneken Pis

Expand Down
15 changes: 11 additions & 4 deletions workflows/structural.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -300,19 +300,26 @@ workflow STRUCTURAL {
no_sex: !meta.sex
}

def ch_samplegender_multi = ch_samplegender_input.no_sex
.multiMap { meta, cram, crai, small_variants ->
cram: [ meta, cram, crai ]
other: [ meta, small_variants ]
}

NGSBITS_SAMPLEGENDER(
ch_samplegender_input.no_sex,
ch_samplegender_multi.cram,
ch_fasta,
ch_fai,
"xy"
)
ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions.first())

ch_input_sex = NGSBITS_SAMPLEGENDER.out.tsv
.join(ch_samplegender_input.no_sex, failOnDuplicate:true, failOnMismatch:true)
.map { meta, tsv, cram, crai ->
.join(ch_samplegender_multi.cram, failOnDuplicate:true, failOnMismatch:true)
.join(ch_samplegender_multi.other, failOnDuplicate:true, failOnMismatch:true)
.map { meta, tsv, cram, crai, small_variants ->
def new_meta = meta + [sex:get_sex(tsv, meta.sample)]
return [ new_meta, cram, crai ]
return [ new_meta, cram, crai, small_variants ]
}
.mix(ch_samplegender_input.sex)
} else {
Expand Down
Loading