Ingest from Pathoplexus, adapt phylogenetic to use Pathoplexus accessions

[corneliusroemer]

Description of proposed changes

• Switch Ingest to use Pathoplexus as data source.
• Adapt Phylogenetic to work with Pathoplexus data

Trial build previews

• https://next.nextstrain.org/staging/trial/ppx/mpox/clade-IIb
• https://next.nextstrain.org/staging/trial/ppx/mpox/all-clades
• https://next.nextstrain.org/staging/trial/ppx/mpox/clade-I
• https://next.nextstrain.org/staging/trial/ppx/mpox/lineage-B.1

How to trigger actions for branch

Ingest:

gh workflow run --ref ppx fetch-and-ingest-branch.yaml

Builds:

for build in clade-i hmpxv1-big hmpxv1 mpxv;
do gh workflow run --ref ppx -f trial_name=ppx rebuild-$build.yaml; 
done

TODO

• Surface link to Genbank
• Fix ncbi.ndjson.zst -> ppx.ndjson.zst
• Db of original submission coloring
• Link to group for PPX data
• For all-clades use all (decent quality) IIa data
• Investigate/exclude outliers
• Potentially mask more problematic areas if outliers have localized mutation clusters
• Root of all-clades trial build is IIb?
• Mention in README and description that data is not guaranteed to be stable, one should download if one wants stability.

Related issue(s)

Resolves #331

Checklist

• Checks pass
• Update changelog