Merge pull request #1151 from nf-core/fix_gtf_flexibility

fix to #1150: reinstate conditional
nf-core · Jan 4, 2024 · cd3a4f5 · cd3a4f5
2 parents b4c6c69 + 456b11b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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
 

diff --git a/bin/tx2gene.py b/bin/tx2gene.py
@@ -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