galaxyproject / galaxyproject/loom

Orbit: preserve/validate unique sample labels before launching DESeq2 (generic labels cause failures)

Open
#288 0 comments 0 reactions 0 assignees View on GitHub
enhancement
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

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