Skip to content
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

fix to #1150: reinstate conditional #1151

Merged
merged 2 commits into from
Jan 4, 2024
Merged

fix to #1150: reinstate conditional #1151

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
05cc397
fix to #1150
pinin4fjords Jan 4, 2024
456b11b
Update CHANGELOG.md
pinin4fjords Jan 4, 2024
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 @@ -25,6 +25,7 @@ Special thanks to the following for their contributions to the release:
- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners
- [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Fix and patch version commands for Fastp, FastQC and UMI-tools modules ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
- [PR #1150](https://github.com/nf-core/rnaseq/pull/1150) - Be more flexible on attribute values in GTFs ([#1132](https://github.com/nf-core/rnaseq/issues/1132))
- [PR #1151](https://github.com/nf-core/rnaseq/pull/1151) - fix to #1150: reinstate conditional

### Parameters

Expand Down
2 changes: 1 addition & 1 deletion bin/tx2gene.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ def discover_transcript_attribute(gtf_file: str, transcripts: Set[str]) -> str:
attributes_str = cols[8]
attributes = dict(re.findall(r'(\S+) "(.*?)(?<!\\)";', attributes_str))

votes.update(key for key, value in attributes.items())
votes.update(key for key, value in attributes.items() if value in transcripts)

if not votes:
# Log a warning if no matching attribute is found
Expand Down
Loading