diff --git a/tests/test_pipeline.py b/tests/test_pipeline.py
index b617186..69f20b8 100644
--- a/tests/test_pipeline.py
+++ b/tests/test_pipeline.py
@@ -28,13 +28,20 @@ def run_pipline(registration_config_path, registration_snakefile, transform_conf
     # Generate deformed data
     deform_test_data(config=registration_config, enable_aniso=enable_aniso, enable_elastic=enable_elastic)
 
+    registration_config["log_dir"] = str(test_dir)
+    registration_config["final_transform_path"] = str(final_transform_path)
+    registration_config["ILP"]["max_dist"] = 10
+
+    tmp_config_path = test_dir / "registration.yaml"
+    with open(tmp_config_path, "w") as f:
+        yaml.dump(registration_config, f)
+
     # Run registration snakemake workflow
     result = subprocess.run(
         [
             "snakemake",
             "--snakefile", registration_snakefile,
-            "--configfile", registration_config_path,
-            "--config", f"log_dir={test_dir}", f"final_transform_path={final_transform_path}",
+            "--configfile", tmp_config_path,
             "--cores", str(cores),
         ],
         check=True,