docs: document nextalign-like use-case

[ivan-aksamentov]

Related: nextstrain/seasonal-cov#2

After release of Nextclade v3 and removal of a standalone nextalign binary, some older workflows relying on Nextalign are left in an awkward state.

There is a migration guide and it's linked in the docs, but there is no dedicated section in the docs about the alignment-only use-cases outside of migration. And the old Nextalign docs are now 404.

We should probably document the Nextalign-like usage in the main Nextclade docs, i.e. using Nextclade v3 without a dataset and providing individual files using --input-* args instead. The invocation of Nextclade v3 with individual args is mostly the same or is very similar to what Nextalign v2 invocation used to be. And I believe that swapping nextclade in place of nextalign executable should either work or produce somewhat informative errors.

Documenting it better would allow for smoother transition to v3 for v1 and v2 users and also highlight that Nextclade v3 can be used as an aligner even where there's no dataset for a particular organism.

Would be amazing if the old links to the Nextalign docs can somehow redirect to the new docs. Or perhaps we could create a deprecation/removal page on that address, with explanation of how to migrate.

[victorlin]

the old Nextalign docs are now 404.
…
Would be amazing if the old links to the Nextalign docs can somehow redirect to the new docs.

Not sure which links you are referring to, but we already have a redirects system on other RTD projects (e.g. Augur) - it can be easily set up here too.