Document the workflow results script

[sjspielman]

Towards #428 (but not 100% actually sure if it closes it? Note also that I opened #502 for later).

This PR documents the results download script by adding a section, along with a little rearrangement, to the "getting access to data" doc. I tried to mostly mirror the way we describe the data download script, and I added a stub reminder to link in forthcoming nf docs. I also added a link to these docs in the "documenting your analysis" page as a reminder that all input data needs to be documented.

There's one spot with a clear request for reviewer phrasing support, but of course more generally let me know about phrasing/organization throughout! Are there spots I should add more details or context?

To facilitate the docs 🎢 ahead of us, I also modified the links and spell check GHAs to run on PRs to the reproducibility branch.

[sjspielman]

To facilitate the docs 🎢 ahead of us, I also modified the links and spell check GHAs to run on PRs to the reproducibility branch.

This was taken care of separately in #510 in the meantime

[sjspielman]

It seems to be missing a discussion of test data results files though, which we should include.

Is there additional information I need beyond what's here to document this, and if so where can I find that additional info? https://github.com/AlexsLemonade/OpenScPCA-nf/blob/main/readme-internal.md

[jashapiro]

It seems to be missing a discussion of test data results files though, which we should include.

Is there additional information I need beyond what's here to document this, and if so where can I find that additional info? https://github.com/AlexsLemonade/OpenScPCA-nf/blob/main/readme-internal.md

I meant documenting the --test-data option, which is parallel to the option in download data. It contains the results of running the workflow on the test data, and will be used for automated testing of modules, as with the download data script option.

[sjspielman]

Thanks for the thorough review! I believe I've gotten all the feedback here, and either way it's definitely updated enough to be ready for another look.

[jashapiro]

You added a bunch of extra stuff with your latests commits/merges. You will need to revert a bunch, but in this case I might even go back to an earlier commit and force push to remove all reference to the extra files here.

[sjspielman]

You added a bunch of extra stuff with your latests commits/merges

Omg I merged in main thinking I was in main................................................................. Training week brain. I'm on it.

[sjspielman]

@jashapiro merge reverted 😬 ... would you prefer I do a harder reset here, or is this fine?