diff --git a/cnvpipelines.py b/cnvpipelines.py
index e282b99e015f329178115c70508a836230fc20ff..df0fd36a00a55911f25424f1819152a2c4f895d3 100755
--- a/cnvpipelines.py
+++ b/cnvpipelines.py
@@ -703,6 +703,10 @@ class CnvPipeline:
                     return False
             else:
                 self._rerun_tools(new_tools=tools)
+                # Remove done files
+                done_files = glob(os.path.join(self.wdir, ".done*"))
+                for done_f in done_files:
+                    os.remove(done_f)
                 if self.config_data["batches"] != batches:
                     print("Error: rerun with a different number of batch size not allowed. Exiting...", file=sys.stderr)
                     exit(1)