AlexsLemonade / AlexsLemonade/OpenScPCA-nf
Include more projects in the stub profile
- Dominant language
- R
- Stars
- 2
- Forks
- 0
- PR merge metrics
- No merged PRs in 30d
Description
Currently, our `testing` and `stub` profiles only use project `SCPCP000012`:
https://github.com/AlexsLemonade/OpenScPCA-nf/blob/09a96997a81ac80bd1080d5a97385a8026f87387/nextflow.config#L78
https://github.com/AlexsLemonade/OpenScPCA-nf/blob/09a96997a81ac80bd1080d5a97385a8026f87387/nextflow.config#L114
This is fine for modules that run on all (or no) samples, but it also means that modules that are specific to a project aren't getting fully run during testing. Currently this includes `cell-type-ewings` and (the in-progress module which is how I noticed this) `cell-type-neuroblastoma-04`.
We could either add these two projects (`SCPCP000015` and `SCPCP000004`) into the profiles, or figure out a different approach to ensure we are testing all components of all modules, e.g. implementing a way to pass in samples or so.
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by reviewing nextflow.config at the profile definitions around lines 78 and 114, then compare the project-specific modules named in the issue. Decide whether adding SCPCP000015 and SCPCP000004 is sufficient or whether sample selection needs a different approach. Done means testing covers all components of the project-specific modules, including cell-type-ewings and cell-type-neuroblastoma-04.
Written by the indexing model from the issue text.
Assessment
- Domain
- build-system, testing
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100