RNAseq on Cavatica tutorial

[s-canchi]

PR Checklist

• Release label added
• PR category label added
• PR mergeable
• Clean build logs
• Linked related issues
• Colorblindness test https://www.toptal.com/designers/colorfilter/

PR Description

This PR adds the RNAseq on Cavatica tutorial along with:

• added the tutorial to Bioinformatics index
• made some styling changes for the tutorial
• added some extra pymarkdown extensions

Preview link
https://cfde-training-and-engagement--316.com.readthedocs.build/en/316/Bioinformatics-Skills/RNAseq-on-Cavatica/rna_seq_1/

Review format

In comments and I will edit the lessons myself.

Timeline

Expect merge for Feb release

[github-actions]

Reviewer Checklist
- [ ] spelling and grammar
- [ ] successful run of all installation and code chunks
- [ ] sufficient explanation and details for the tutorial content
- [ ] code syntax and naming convention
- [ ] adherence of tutorial format to style guide
- [ ] functional links (inter and intra)
- [ ] accessible hyperlink text

[marisalim]

@s-canchi

Great tutorial! This will be good material for KF/Cavatica workshops. I reviewed the tutorial on Firefox with KF/Cavatica accounts that are NOT linked to eRA Commons ID.

A few general comments -

• The vidlets are very helpful! I'd switch the order of appearance and add a note at the beginning of the lesson(s) that we recommend watching vidlets first, then following written instructions. I missed some steps when I started with the written instructions.
• For tag, file, and excel column names, tell ppl to use the same names as in the tutorial to avoid naming issues in the app inputs and running R script sections.

I have a lot of specific notes & suggestions per page here --> https://hackmd.io/qR9-1yA2QNKv71kXLxPZHw?edit

[s-canchi]

Thanks @marisalim for all the comments and suggestions! Glad to know it worked in an non eRA account :)

[jeremywalter]

I have gone through this a few times now and successfully completed all sections but 3b of the data cruncher. I ran the installation chunk successfully but the pcaExplorere code would not run as it does in the video, instead giving me this output:

[s-canchi]

Thank you @marisalim @jeremywalter !! This is getting merged in :)