diff --git a/src/sophios/main.py b/src/sophios/main.py
index 4b267e96..b1d91cca 100644
--- a/src/sophios/main.py
+++ b/src/sophios/main.py
@@ -155,11 +155,11 @@ def main() -> None:
             sys.exit(1)
         rose_tree = compiler_info.rose
     rose_tree = plugins.cwl_prepend_dockerFile_include_path_rosetree(rose_tree)
-    io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
 
     if args.partial_failure_enable:
         rose_tree = plugins.cwl_update_outputs_optional_rosetree(rose_tree)
-        io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
+
+    io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
 
     if args.graphviz:
         if shutil.which('dot'):