diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index a8ce20e..4a72f5f 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -232,15 +232,26 @@ 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
+        if: ${{ hashFiles('nextstrain-pathogen.yaml','ingest/Snakefile','ingest/build-configs/ci/config.yaml') != '' }}
+        run: nextstrain build ingest --config ingest/build-configs/ci/config.yaml ${{ inputs.build-args }}
 
-      - run: nextstrain build . ${{ inputs.build-args }}
-
-      - if: always()
+      - name: Upload ingest artifact
+        if: ${{ hashFiles('nextstrain-pathogen.yaml','ingest/Snakefile','ingest/build-configs/ci/config.yaml') != '' }}
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
+          name: ingest-${{ inputs.artifact-name }}-${{ matrix.runtime }}
           path: |
-            auspice/
             results/
             benchmarks/
             logs/