Migrate GitHub wiki into docs/ folder

[wsowens]

All of our protocols and pipeline details are currently contained in a GitHub wiki. Unfortunately, even though the GitHub wiki is just another git repository, GitHub offers no sort of formal review process for editing wiki pages. We have no way to flag issues, assign responsibility, or review updates.

There's two avenues we can take here, one is the tried-and-true approach of adding a docs/ folder to your repository. This is pretty straightforward and intuitive, but lacks a table of contents and may be off-putting to an audience less acquainted with software documentation practices.

Another approach is creating a second GitHub repository for octopus.wiki and pushing updates to octopus.wiki using GitHub actions (various implementations discussed here). This feels a little brittle and unconventional to me, but makes the a user experience a bit smoother. My main concern is that maintaining the documentation will become tedious at that point, and we're less likely to keep it up-to-date.

This PR implements the first solution, but I'm interested in hearing opinions on the two options.

[wsowens]

To add to this discussion, looking at a number of popular, well-documented repositories, it seems like contributors typically opt for approach 1 (the docs/ approach). Examples:

• snakemake
• youtube-dl
• dplyr
• clap-rs
• biopython

I've found some projects that use a Wiki (e.g. nektos/act) but any that actually use the second approach I outlined above.

[bryanliujiang]

I agree it would be best to implement the /docs approach to keep this repository a one-stop shop for everything OCTOPUS-related. Closing for now. In the future, we could add maybe a printable PDF or something summarizing the protocol.

[bryanliujiang]

I agree it would be best to implement the /docs approach to keep this repository a one-stop shop for everything OCTOPUS-related. Closing for now. In the future, we could add maybe a printable PDF or something summarizing the protocol.