Make ADJUST_BATCH_EFFECT optional when phenotypes are present
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Nextflow
- Stars
- 9
- Forks
- 6
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
When user just wants to compare two or more experimental conditions it makes no sense to run ADJUST_BATCH_EFFECT, as there will be simply no phenotypes to use at that stage. We can make this optional
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating where ADJUST_BATCH_EFFECT and phenotype inputs are handled in the workflow. Check how comparisons between experimental conditions are currently configured. Done means users can run that comparison without providing phenotypes or running ADJUST_BATCH_EFFECT, while existing phenotype-based behavior remains available.
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
- 45/100