allow gzipped FASTAs and GTFs when using STAR
Open
enhancement
- Dominant language
- R
- Stars
- 10
- Forks
- 9
- PR merge metrics
- No merged PRs in 30d
Description
STAR by default does not support gzipped FASTAs and GTFs. So the WASP subworkflow just fails if the user provides files that are gzipped. But it would be great if the pipeline automatically handled the gzipped case. [Here](https://bioinformatics.stackexchange.com/a/3641) are some potential workarounds.
Contributor guide
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Research direction
Start with the WASP subworkflow and trace how the STAR inputs receive the FASTA and GTF paths. Check the linked workaround and verify the pipeline succeeds when both files are gzipped, while preserving the existing behavior for uncompressed files.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100