diff --git a/ingest/README.md b/ingest/README.md
index 3d8c451..371ce02 100644
--- a/ingest/README.md
+++ b/ingest/README.md
@@ -31,7 +31,7 @@ This will produce two files (within the `ingest` directory):
 Run the complete ingest pipeline and upload results to AWS S3 with
 
 ```sh
-nextstrain build . --configfiles config/config.yaml config/optional.yaml
+nextstrain build . --configfiles config/config.yaml build-configs/nextstrain-automation/config.yaml
 ```
 
 ### Adding new sequences not from GenBank
diff --git a/ingest/defaults/optional.yaml b/ingest/build-configs/nextstrain-automation/config.yaml
similarity index 100%
rename from ingest/defaults/optional.yaml
rename to ingest/build-configs/nextstrain-automation/config.yaml
diff --git a/ingest/rules/upload.smk b/ingest/build-configs/nextstrain-automation/upload.smk
similarity index 100%
rename from ingest/rules/upload.smk
rename to ingest/build-configs/nextstrain-automation/upload.smk