galaxyproject / galaxyproject/loom
Orbit: preserve/validate unique sample labels before launching DESeq2 (generic labels cause failures)
- Dominant language
- TypeScript
- Stars
- 14
- Forks
- 12
- Avg merge
- 6d 5h
- Merged PRs (30d)
- 17
Description
In a DEG run, count tables carried generic/duplicate labels (e.g. `0`, `1`, `2`, or identical `Counts Table` names), producing non-unique identifiers that prevented DESeq2 from running. Orbit eventually worked around it by downloading and re-uploading the count tables with unique names, but that's a manual detour.
Orbit should preserve original sample identifiers from the upstream collection and validate that labels are unique (and non-generic) before launching DESeq2, rather than failing and recovering by re-upload.
Related to #208 (collection handling) and to the fold-change interpretation issue #289.
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by tracing Orbit's count-table collection handling into the DESeq2 launch path, using the relationship to #208 as context. Confirm where upstream sample identifiers are lost and where labels can be checked; done means original identifiers are preserved and duplicate or generic labels are rejected before DESeq2 starts.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- typescript
- Domain
- bioinformatics, data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 50/100