STAR index wrapper with GFF
andreott opened this issue · 1 comments
andreott commented
Is your feature request related to a problem? Please describe.
When using STAR index with a GFF instead of GTF file, the flag --sjdbGTFtagExonParentTranscript Parent needs to be passed.
Describe the solution you'd like
Obviously the user can provide the appropriate argument as extra. I just want to explore whether you would consider to integrate this logic into the wrapper - checking for file extension and in case of gff(3), add the flag. Or maybe another named parameter like annot_format which then translates into the command line argument.
If you like the idea, I can also provide a PR.
fgvieira commented
Sounds good! Just make a PR and I'll look into it.