diff --git a/nextstrain-pathogen.yaml b/nextstrain-pathogen.yaml
index 7a31ac3..16abff0 100644
--- a/nextstrain-pathogen.yaml
+++ b/nextstrain-pathogen.yaml
@@ -6,5 +6,13 @@
 # This file's *contents* is the "registration metadata" for the pathogen repo,
 # used by `nextstrain setup` and `nextstrain run`.
 ---
-compatibility:
-  nextstrain run: true
\ No newline at end of file
+workflows:
+  ingest:
+    compatibility:
+      nextstrain run: True
+  phylogenetic:
+    compatibility:
+      nextstrain run: True
+  nextclade:
+    compatibility:
+      nextstrain run: True