From a840e9268861b8ffd12ad1756926a81c6cd9bd94 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] Add `ingest` build step [#89]

---
 .github/workflows/pathogen-repo-ci.yaml | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index a8ce20e..b4af42f 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -232,15 +232,30 @@ jobs:
         with:
           runtime: ${{ matrix.runtime }}
 
+  ingest:
+    name: ingest (${{ matrix.runtime }})
+    needs: [configuration, build]
+    strategy:
+      fail-fast: false
+      matrix:
+        runtime: ${{ fromJSON(needs.configuration.outputs.runtimes) }}
+    runs-on: ubuntu-latest
+    continue-on-error: ${{ inputs.continue-on-error }}
+    steps:
+      - name: Run ingest
+        run: |
+          if [[ -f nextstrain-pathogen.yaml && -f ingest/Snakefile && -f ingest/build-configs/ci/config.yaml]]; then
+            nextstrain build ingest --config build-configs/ci/config.yaml ${{ inputs.build-args }}
+          else
+            echo "Skipping ingest build due to one or more missing files."
+          fi
 
-      - run: nextstrain build . ${{ inputs.build-args }}
-
-      - if: always()
+      - name: Upload ingest artifact
+        if: always()
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
+          name: ingest-${{ inputs.artifact-name }}-${{ matrix.runtime }}
           path: |
-            auspice/
             results/
             benchmarks/
             logs/