From 7db401b27a0b1bf6ba6b5dadefc8cc9640530dd1 Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Mon, 25 Mar 2024 17:21:09 -0700
Subject: [PATCH] WIP: ingest-to-phylo workflow

---
 .github/workflows/ingest-to-phylogenetic.yaml | 54 +++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 .github/workflows/ingest-to-phylogenetic.yaml

diff --git a/.github/workflows/ingest-to-phylogenetic.yaml b/.github/workflows/ingest-to-phylogenetic.yaml
new file mode 100644
index 0000000..b709342
--- /dev/null
+++ b/.github/workflows/ingest-to-phylogenetic.yaml
@@ -0,0 +1,54 @@
+name: Ingest to phylogenetic
+
+on:
+  workflow_dispatch:
+
+jobs:
+  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 \
+          ingest \
+            upload_all \
+            --configfile build-configs/nextstrain-automation/config.yaml
+      # Specifying artifact name to differentiate ingest build outputs from
+      # the phylogenetic build outputs
+      artifact-name: ingest-build-output
+      artifact-paths: |
+        ingest/results/
+        ingest/benchmarks/
+        ingest/logs/
+        ingest/.snakemake/log/
+
+  # TKTK check for new data from ingest
+  # This can potentially interface with GH and/or S3?
+  # 1. Check last automated run's GH artifact output and diff with current S3 files
+  # 2. Check S3's previous version of outputs and diff with current S3 files
+
+  # TKTK phylo workflow
+  # Just realized the phylo workflow does not have automated build uploads
+
+  # phylogenetic:
+  #   needs: [ingest]
+  #   permissions:
+  #     id-token: write
+  #   uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+  #   secrets: inherit
+  #   with:
+  #     runtime: docker
+  #     run: |
+  #       nextstrain build \
+  #         --env AWS_ACCESS_KEY_ID \
+  #         --env AWS_SECRET_ACCESS_KEY \
+  #         phylogenetic \
+  #           --configfile build-configs/nextstrain-automation/config.yaml