Update existing pathogen repos to vendor ingest scripts

[joverlee521]

Context

Depends on #3

Once we've decided on how to vendor the centralized ingest scripts, we should update the existing pathogen builds to use the ingest scripts.

This will probably be better to do as an iterative process that happens in parallel with #1.

Description

Repos that should be updated to vendor the ingest scripts:

• Use nextstrain/ingest mpox#164
• Use nextstrain/ingest ncov-ingest#412
• [ ] ncov Skipping since not worth complexity
• Use nextstrain/ingest rsv#32
• Use nextstrain/ingest hbv#5
• Seq counts workflow forecasts-ncov#60 + Clean up workflows forecasts-ncov#62

The following repos have WIP PRs for adding ingest to their workflows that can be updated to vendor the scripts:

• Copy ingest dengue#13
• Persephone zika#28

[victorlin]

To start things off, I'm going to try this for the monkeypox repo: nextstrain/mpox#164

[victorlin]

Is the ncov repo worth including in this initial effort? It has no use for the ingest-specific scripts, but does use upload-to-s3+sha256sum.

From 690fa99:

The copy of this script in ncov² has diverged enough that I think it's not worth it to incorporate changes here.
² https://github.com/nextstrain/ncov/blob/ba9953f8a61d239176e960b9b2efb925b5dff84b/scripts/upload-to-s3

I assume ncov should keep using its own copy of upload-to-s3. That leaves sha256sum as the only script to switch over to. This is what that would look like: nextstrain/ncov@fcd7327...79af5ca

The added subrepo complexity in the ncov repo just for the sha256sum script is not worth it to me.

[joverlee521]

The added subrepo complexity in the ncov repo just for the sha256sum script is not worth it to me.

Agreed! We can skip the ncov repo.

[victorlin]

Assigning @j23414 for dengue and zika.