GHA: Automated live (rendered) versions of the notebooks

[alexslemonade-docs-bot]

Description:

This PR auto-generated from github actions running make-live.R with:

• The latest notebooks on the master branch
• The latest docker image on Dockerhub

Instruction for reviewers:

Make sure that all the notebooks have been made into _live versions appropriately and have the updates you expect.

[jaclyn-taroni]

Per team meeting

@jashapiro to review intro to R/Tidyverse material and 2nd half of RNA-seq
@cansavvy to review 1st half of RNA-seq
@jaclyn-taroni to review pathway analysis

All other 👀 welcome!

[jashapiro]

A note for reviewers: There seems to be a bug (or at least behavior unexpected to me) with Rmarkdown::render() that results in character vectors printing oddly when called on their own. You can see this at the following htmlpreview link:
https://htmlpreview.github.io/?https://github.com/AlexsLemonade/training-modules/blob/7517d4d1b1d288fe8920e337ee8f21c0d71db8fe/RNA-seq/02-gastric_cancer_tximeta.nb.html#file-names

In particular, the character vector prints twice, once with no quotes and lots of space. I have posted a couple places to see if there is a quick fix, but have gotten no response as yet. So for now I would say we should let this pass: it does not affect how these notebooks will render in use, only how they look in this repo.

[cansavvy]

I've only looked at the RNA-seq notebooks: the -live and the rendered versions. The only comments I have are:

• I'm noticing the same double print out issue @jashapiro mentioned about 02-gastric_cancer_tximeta.nb.html also happening in 05-nb_cell_line_DESeq2.nb.html:
  At least the problem is consistent.

• Should 04-nb_cell_line_tximeta.Rmd have Learning Objectives? Feels odd that its the only one without?

[jaclyn-taroni]

Pathway analysis stuff LGTM

[jashapiro]

• Should 04-nb_cell_line_tximeta.Rmd have Learning Objectives? Feels odd that its the only one without?

I don't think we need it to, since that is the guided exercise and introduces no new concepts.

[jashapiro]

This all looks good, but is awaiting a rerun (in progress) with the small rendering change to add max.print.

[jashapiro]

Approving this, as it seems to have everything we need. Again, you have about 20 minutes before I push the button!