diff --git a/snakemake/config.smk b/snakemake/config.smk
index 15727b0..ada7c1c 100644
--- a/snakemake/config.smk
+++ b/snakemake/config.smk
@@ -156,6 +156,11 @@ def write_config(path):
     os.makedirs(os.path.dirname(path), exist_ok=True)
 
     with open(path, 'w') as f:
-        yaml.dump(config, f, sort_keys=False)
+        yaml.dump(config, f, sort_keys=False, Dumper=NoAliasDumper)
 
     print(f"Saved current run config to {path!r}.", file=sys.stderr)
+
+
+class NoAliasDumper(yaml.SafeDumper):
+    def ignore_aliases(self, data):
+        return True