From d60bfb09db1b8242eaaf7cabed671b75621adc32 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Fri, 31 May 2024 11:33:29 -0700
Subject: [PATCH] Refactor `pathogen-repo-ci` to be smarter [#89]

---
 .github/workflows/pathogen-repo-ci.yaml  | 21 +++++++------
 actions/run-nextstrain-build/action.yaml | 39 ++++++++++++++++++++++++
 2 files changed, 50 insertions(+), 10 deletions(-)
 create mode 100644 actions/run-nextstrain-build/action.yaml

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index a8ce20e..91ac428 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -232,16 +232,17 @@ jobs:
         with:
           runtime: ${{ matrix.runtime }}
 
+      - name: Run ingest
+        uses: nextstrain/.github/actions/run-nextstrain-build@update-ci-89
+        with:
+          step: ingest
 
-      - run: nextstrain build . ${{ inputs.build-args }}
+      - name: Run phylogenetic
+        uses: nextstrain/.github/actions/run-nextstrain-build@update-ci-89
+        with:
+          step: phylogenetic
 
-      - if: always()
-        uses: actions/upload-artifact@v4
+      - name: Run nextclade
+        uses: nextstrain/.github/actions/run-nextstrain-build@update-ci-89
         with:
-          name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
-          path: |
-            auspice/
-            results/
-            benchmarks/
-            logs/
-            .snakemake/log/
+          step: nextclade
diff --git a/actions/run-nextstrain-build/action.yaml b/actions/run-nextstrain-build/action.yaml
new file mode 100644
index 0000000..4ade117
--- /dev/null
+++ b/actions/run-nextstrain-build/action.yaml
@@ -0,0 +1,39 @@
+name: run-nextstrain-build
+description: >-
+  Runs a single `nextstrain build` command in a given sub-directory of
+  a pathogen repo. Must be provided with the name of the
+  sub-directory.
+
+inputs:
+  step:
+    description: The name of the sub-directory to run the build from
+    type: string
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - id: Run ${{ inputs.step }}
+      env:
+        STEP: ${{ inputs.step }}
+      run: |
+        if [[ -f nextstrain-pathogen.yaml && -f $STEP/Snakefile && -f $STEP/build-configs/ci/config.yaml ]]; then
+          nextstrain build $STEP --configfile build-configs/ci/config.yaml
+        else
+          echo "Skipping $STEP build due to one or more missing files."
+          for i in nextstrain-pathogen.yaml $STEP/Snakefile $STEP/build-configs/ci/config.yaml; do
+            ! test -f $i && echo missing $i
+          done
+        fi
+      shell: bash
+
+    - id: Upload ${{ inputs.step }} artifact
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{inputs.step }}-outputs-${{ matrix.runtime }}
+        path: |
+          ${{ inputs.step }}/results/
+          ${{ inputs.step }}/benchmarks/
+          ${{ inputs.step }}/logs/
+          ${{ inputs.step }}/.snakemake/log/