AlexsLemonade / AlexsLemonade/OpenScPCA-nf

Include more projects in the stub profile

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R
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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

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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

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