AlexsLemonade / OpenScPCA-analysis

An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
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Add module GHA doc #528

Closed sjspielman closed 1 week ago

sjspielman commented 2 weeks ago

Closes #517

This PR adds documentation for module GHAs. For the first round of review here, please let me know high-level organizational and content comments, and then we can get finer-grained from there!

A couple things to note:

jashapiro commented 2 weeks ago
  • I wanted to find somewhere else in docs to incorporate the insight that you should use arguments for specifying input data paths, to make modules flexible enough to run with test data. I wasn't sure where exactly to put that? It could go into notebook-structure.md or script-structure.md, or somewhere else?

If people use relative input paths and files in data/current/ this should generally be taken care of automatically. I don't know if we have specific instructions to use that path, but that is what I would emphasize. There should not generally be variable changes needed for running tests (though there will always be some things that get broken by not having expected results)

sjspielman commented 1 week ago

Sigh, I keep merging in main. Fixed. But sigh. https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/528/commits/c6252a34c4d34397b621d7384a3bcf54ae6a8f26.