ingest-to-phylogenetic: Add phylogenetic job

The phylogenetic workflow will run after the ingest workflow has
completed successfully to use the latest available data.

Subsequent commits will check if the ingest results included new
data to only run the phylogenetic workflow when there's new data.

.github/workflows/ingest-to-phylogenetic.yaml

@@ -38,3 +38,34 @@ jobs:
         ingest/benchmarks/
         ingest/logs/
         ingest/.snakemake/log/
+
+  # TKTK check if ingest results include new data
+  # potentially use actions/cache to store Metadata.sha256sum of S3 files
+
+  phylogenetic:
+    needs: [ingest]
+    permissions:
+      id-token: write
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    secrets: inherit
+    with:
+      # Starting with the default docker runtime
+      # We can migrate to AWS Batch when/if we need to for more resources or if
+      # the job runs longer than the GH Action limit of 6 hours.
+      runtime: docker
+      run: |
+        nextstrain build \
+          --env AWS_ACCESS_KEY_ID \
+          --env AWS_SECRET_ACCESS_KEY \
+          phylogenetic \
+            deploy_all \
+            --configfile build-configs/nextstrain-automation/config.yaml
+      # Specifying artifact name to differentiate ingest build outputs from
+      # the phylogenetic build outputs
+      artifact-name: phylogenetic-build-output
+      artifact-paths: |
+        phylogenetic/auspice/
+        phylogenetic/results/
+        phylogenetic/benchmarks/
+        phylogenetic/logs/
+        phylogenetic/.snakemake/log/