Skip to content

Bug: KRAKENUNIQ reads channel #630

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
merged 2 commits into from
Aug 14, 2025
Merged

Bug: KRAKENUNIQ reads channel #630

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4b9a3e3
Fix krakenuniq reads channel: profiling.nf
LilyAnderssonLee Aug 14, 2025
daf9135
update CHANGELOG.md
LilyAnderssonLee Aug 14, 2025
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 @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#592](https://github.com/nf-core/taxprofiler/pull/592) improved JSON schema for better validation (by @microlei)
- [#604](https://github.com/nf-core/taxprofiler/pull/604) KrakenUniq no longer fails due to pathname splitting during batching when only single sample supplied (by @AlexHoratio)
- [#612](https://github.com/nf-core/taxprofiler/pull/616) Fix bug with bracken results being shown in MuktiQC for long read data every if bracken not supported for long reads (added by @jfy133 and @sofstam )
- [#630](https://github.com/nf-core/taxprofiler/pull/630) Fix a bug in KRAKENUNIQ reads channel where a single-element list containing a / in the path was being split incorrectly, causing unexpected multiple list elements.

### `Changed`

Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/profiling.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -373,7 +373,7 @@ workflow PROFILING {
// We bundle the sample identifier with the sequencing files to undergo batching.
def prefix = params.perform_runmerging ? meta.id : "${meta.id}_${meta.run_accession}"
prefix = meta.single_end ? "${prefix}.se" : "${prefix}.pe"
[[id: db_meta.db_name, single_end: meta.single_end, seqtype: seqtype], [reads] + [prefix], db_meta, db]
[[id: db_meta.db_name, single_end: meta.single_end, seqtype: seqtype], [reads].flatten() + [prefix], db_meta, db]
}
.groupTuple(by: [0, 2, 3])
.flatMap { single_meta, reads, db_meta, db ->
Expand Down