gtffilter: add support for non-Ensembl GTF files#12393
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kanishkanandhkumar wants to merge 3 commits into
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gtffilter: add support for non-Ensembl GTF files#12393kanishkanandhkumar wants to merge 3 commits into
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| Args: | ||
| data (dict): The dictionary to format. | ||
| indent (int): The current indentation level. | ||
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| Returns: | ||
| str: A string formatted as YAML. |
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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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This PR updates modules/nf-core/custom/gtffilter/templates/gtffilter.py to support non-Ensembl GTF annotations (e.g., NCBI/RefSeq, GENCODE, FlyBase, TAIR).
Summary of fixes:
Header/Comment preservation: Updated parsing to retain lines starting with # without triggering column-count validation errors.
Flexible transcript_id matching: Replaced strict Ensembl regex (transcript_id "...") with a flexible regex pattern to match unquoted, single-quoted, and =-separated attributes (e.g., transcript_id=TX123).
Top-level gene retention: Ensured top-level gene feature entries are preserved even when they lack a transcript_id attribute.
Gzip support fix: Fixed tab_delimited() validation so .gtf.gz compressed inputs are properly uncompressed during checking rather than throwing column count errors.
Type of Change
Bug fix (non-breaking change fixing an issue)
New feature
Documentation update
Verification
Ran nf-core modules lint custom/gtffilter locally (Passed 45/45 tests).
Verified python script syntax and execution.