phylogenetic: Use inline root sequence

[joverlee521]

Description of proposed changes

~Explicitly state that the root-sequence.json file is an expected output of the core phylogenetic workflow.~

~This also ensures that the Nextstrain automation rule deploy_all will include the root-sequence.json in the upload.~

Based on feedback from @jameshadfield in https://github.com/nextstrain/zika/pull/56#issuecomment-2058060422

Looking at the existing dataset files on S3, the 8 KiB root-sequence.json is pretty negligible when the main Auspice JSON is only 163 KiB. Nextstrain datasets are limited by the 500MB memory cap in Chrome,¹ so we'd be fine adding the root sequence inline.

This ensures that our uploads will include the root sequence so that they don't get out-of-sync with the main Auspice JSON.

¹ https://github.com/nextstrain/auspice/issues/1622

Related issue(s)

Follow up to https://github.com/nextstrain/measles/pull/21 Similar to https://github.com/nextstrain/zika/pull/56

Checklist

• [ ] Checks pass

[joverlee521]

Sorry to switch it up on you @kimandrews! I just pushed up new changes to make the root sequence inline so that we no longer have to worry about the root-sequence.json file.

[joverlee521]

Merging since the CI run's outputs include root_sequence in the Auspice JSONs and the datasets looks good in auspice.us

[joverlee521]

Manually deleted cache and triggered a re-run of the ingest-to-phylo workflow.

Once complete

• [x] Remove the existing s3://nextstrain-data/measles_root-sequence.json