Merge branch 'dev' into ensure_notnull_pseudo

Author: pinin4fjords

CHANGELOG.md

@@ -17,8 +17,8 @@ Special thanks to the following for their contributions to the release:
 
 - [PR #1123](https://github.com/nf-core/rnaseq/pull/1123) - Overhaul tximport.r, output length tables
 - [PR #1124](https://github.com/nf-core/rnaseq/pull/1124) - Ensure pseudoaligner is set if pseudoalignment is not skipped
-- [PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true
-- [#1125](https://github.com/nf-core/rnaseq/issues/1125) - Pipeline fails if transcript_fasta not provided and skip_gtf_filter = true
+- [[PR #1126](https://github.com/nf-core/rnaseq/pull/1126)] [[#1125](https://github.com/nf-core/rnaseq/issues/1125)] - Pipeline fails if transcript_fasta not provided and `skip_gtf_filter = true`.
+- [[PR #1127](https://github.com/nf-core/rnaseq/pull/1127)] - Enlarge sampling to determine the number of columns in `filter_gtf.py` script.
 
 ## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17
 

bin/filter_gtf.py

@@ -23,7 +23,7 @@ def extract_fasta_seq_names(fasta_name: str) -> Set[str]:
 def tab_delimited(file: str) -> float:
     """Check if file is tab-delimited and return median number of tabs."""
     with open(file, "r") as f:
-        data = f.read(1024)
+        data = f.read(102400)
         return statistics.median(line.count("\t") for line in data.split("\n"))