Automate ingest and phylogenetic workflows

[j23414]

Description of proposed changes

Coordinated with @joverlee521 to copy commits from zika PR: https://github.com/nextstrain/zika/pull/52

Adds a single GH Action workflow to automate the ingest and phylogenetic workflows, set to run daily at the same time as the automated mpox ingest.

Uses GH Action caches to store hash of ingest results' Metadata.sha256sum values added to the S3 metadata within upload-to-s3. If the cache contains a match from previous runs of the GH Action workflow, then the workflow will skip the phylogenetic job.

See commits for details.

Related issue(s)

Based on discussion in https://github.com/nextstrain/pathogen-repo-guide/issues/25

• https://github.com/nextstrain/zika/pull/52

Checklist

• [x] Checks pass
• [x] Manually trigger first full run

The manual run completed successfully although does not push to the live site since output files do not have "_genome" postfixs in the filenames:

nextstrain remote upload s3://nextstrain-data auspice/dengue_all.json auspice/dengue_denv1.json auspice/dengue_denv2.json auspice/dengue_denv3.json auspice/dengue_denv4.json

Uploading auspice/dengue_all.json as dengue_all.json
Uploading auspice/dengue_denv1.json as dengue_denv1.json
Uploading auspice/dengue_denv2.json as dengue_denv2.json
Uploading auspice/dengue_denv3.json as dengue_denv3.json
Uploading auspice/dengue_denv4.json as dengue_denv4.json

[joverlee521]

Yay, the test run completed with plenty of time to spare for the phylogenetic workflow 🎉

The manual run completed successfully although does not push to the live site since output files do not have "_genome" postfixs in the filenames

I know this will be fixed in https://github.com/nextstrain/dengue/pull/18, but I would just update the phylo outputs with the hardcoded _genome filename in this PR so that the automated builds get surfaced through nextstrain.org.

[joverlee521]

FYI, after the initial trigger with pull_request you should be able to trigger the workflow manually with

gh workflow run ingest-to-phylogenetic.yaml  --ref automate-workflows

[joverlee521]

The dengue workflow is now showing up on the pathogen workflow status page