filter: Expand subsampling docs

[victorlin]

(preview)

Description of proposed changes

Expand subsampling docs with a guide on how to implement multi-pass subsampling¹.

¹ internal subsampling doc definition of "multi-pass subsampling": Subsampling done as multiple calls to a subsampling tool, where intermediate subsamples are created and joined together to create a final/combined sample. It is used to work around limitations on what can be done in a single pass.

Related issue(s)

• Add docs for "tiered" subsampling docs.nextstrain.org#187

Checklist

• Checks pass
• If making user-facing changes, add a message in CHANGES.md summarizing the changes in this PR
• Post-merge: Link to these docs from docs/guides/bioinformatics: Add guide on filtering and subsampling docs.nextstrain.org#192
• Update help text for --exclude/--include (ref)

[huddlej]

These docs have been needed for so long, so thank you for making them a reality, @victorlin. With the exception of some minor typos that @jameshadfield pointed out, you could easily merge this now and it would be a big help to users. I made a few comments below that mostly attempt to clarify the content for new users.

[huddlej]

As a thought experiment, it would be interesting to see how we'd implement these same augur filter subsampling examples with the proposed augur subsample command and config file. I guess it would look a bit like the subsampling block of the build config YAML?

[victorlin]

I've resolved all conversations above. Will merge on any approval.

[joverlee521]

Thank you for the clear and thoughtful docs! It will be nice to be able to point users to these guides 🙏

I found one more typo and left some other non-blocking comments, but I think good to merge whenever you think it's ready.