diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index e753afe..3d45e5a 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -1,11 +1,14 @@
-name: CI
-
-on:
-  - push
-  - pull_request
-
-jobs:
-  ci:
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
-    with:
-      build-args: test_target
+name: CI
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  ci:
+    # Pin pathogen-repo-ci since this repo's file structure does not conform to
+    # to the smart pathogen-repo-ci. It's unclear if it every will completely
+    # conform since this is a collaborative repo with an external group.
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@v0
+    with:
+      build-args: test_target