[FEATURE REQUEST] Adding the `ecophylo` and `trnaseq` workflows to anvi'o docs, and more

[meren]

In addition to artifacts and programs, the anvi'o docs now supports workflows following the PR #1977.

Adding a new workflow is quite straightforward, and every file that needs to be edited to add a new workflow is demonstrated in https://github.com/merenlab/anvio/pull/1977/commits/379ba4351c4aa939f7485af0b765ccded0234ed1.

Since there is already so much documentation, I think it will be quite straightforward to add the ecophylo workflow by @mschecht and the trnaseq workflow by @semiller10 into this. So I propose their addition to this system :)

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We also need to clean up a few things, which I will do, including,

• [ ] Adding the pangenomics and phylogenomics workflows.
• [ ] Updating the anvi'o snakemake workflows tutorial so it reflects the new organization.
• [ ] Editing the workflow descriptions for contigs, metagenomics, pangenomics, and phylogenomics, so the language is smooth and aligned with the tone of the anvi'o docs.

[mschecht]

@meren thanks again for giving workflows a separate documentation infrastructure. I took a swing at this here: https://github.com/merenlab/anvio/tree/ecophylo-artifact-documentation

Should I remove the ecophylo artifact in this branch or would we keep both artifacts?

[mschecht]

@meren can we also have an artifacts_accepted option? I think it's important to document which artifacts are the input to workflows as well e.g. the contigs-worklow should accept a fasta and ecophylo-worflow would accept hmm-list

[meren]

@meren can we also have an artifacts_accepted option?

This is now done, @mschecht.

[ivagljiva]

@meren and/or @mschecht , is this workflow documentation all finished? Can we close this issue? :)

[meren]

Let's keep this open for a little longer :)

Thank you for going through all these issues, Iva!

[mschecht]

Thanks for the ping everyone - I'll run through my current documentation and prepare commits. I know the release timeline is tight.

[mschecht]

Ok I made some minor adjustments but did not push the commit. Let me know if/when it's ok to push :)

[ivagljiva]

Please feel free to push your commits @mschecht. It would be great if you could do it as soon as possible :)