diff --git a/corrlib/git_tools.py b/corrlib/git_tools.py
index b66191b..6569be0 100644
--- a/corrlib/git_tools.py
+++ b/corrlib/git_tools.py
@@ -1,5 +1,6 @@
 import os
 import datalad.api as dl
+import git
 
 GITMODULES_FILE = '.gitmodules'
 
@@ -19,7 +20,10 @@ def move_submodule(repo_path, old_path, new_path):
     """
 
     os.rename(os.path.join(repo_path, old_path), os.path.join(repo_path, new_path))
+
     gitmodules_file_path = os.path.join(repo_path, GITMODULES_FILE)
+
+    # update paths in .gitmodules
     with open(gitmodules_file_path, 'r') as file:
         lines = [line.strip() for line in file]
 
@@ -32,6 +36,8 @@ def move_submodule(repo_path, old_path, new_path):
     with open(gitmodules_file_path, 'w') as file:
         file.write("\n".join(updated_lines))
 
-    with open(repo_path + '/.gitmodules', 'w') as fp:
-        fp.writelines(lines)
+    # stage .gitmodules in git
+    repo = git.Repo(repo_path)
+    repo.git.add('.gitmodules')
+    # save new state of the dataset
     dl.save(repo_path, message=f"Move module from {old_path} to {new_path}", dataset=repo_path)