diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 4c99e29b..58d0dbaf 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -9,8 +9,22 @@ on:
 
 jobs:
   pathogen-ci:
-    # Temporarily use this ref until the commit is merged into the main repo
-    # PR: https://github.com/nextstrain/.github/pull/62 (opened on 2023-09-27)
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@4f3074183d6ab612faed84444eefe08a5ded0c69
+    strategy:
+      matrix:
+        runtime: [docker, conda]
+    permissions:
+      id-token: write
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    secrets: inherit
     with:
-      build-dir: phylogenetic
+      runtime: ${{ matrix.runtime }}
+      run: |
+        nextstrain build \
+          phylogenetic \
+          --configfile profiles/ci/builds.yaml
+      artifact-paths: |
+        phylogenetic/auspice/
+        phylogenetic/results/
+        phylogenetic/benchmarks/
+        phylogenetic/logs/
+        phylogenetic/.snakemake/log/