copy all files when reverting a patch

nf_core/modules/modules_json.py

@@ -799,7 +799,9 @@ def get_patch_fn(self, module_name, repo_url, install_dir):
         )
         return Path(path) if path is not None else None
 
-    def try_apply_patch_reverse(self, module, repo_name, patch_relpath, module_dir):
+    def try_apply_patch_reverse(
+        self, module: str, repo_name: str, patch_relpath: Union[Path, str], module_dir: Union[Path, str]
+    ) -> Path:
         """
         Try reverse applying a patch file to the modified module files
 
@@ -822,17 +824,30 @@ def try_apply_patch_reverse(self, module, repo_name, patch_relpath, module_dir):
             new_files = ModulesDiffer.try_apply_patch(module, repo_name, patch_path, module_dir, reverse=True)
         except LookupError as e:
             raise LookupError(f"Failed to apply patch in reverse for module '{module_fullname}' due to: {e}")
-
-        # Write the patched files to a temporary directory
-        log.debug("Writing patched files to tmpdir")
+        # get all files of the module
+
+        module_files = list(Path(module_dir).rglob("*"))
+        # exclude the patch file
+        log.info(f"Excluding patch file '{patch_path}' from the patched files")
+        unpatched_module_files = [f for f in module_files if f != patch_path]
+        # Write the patched files and rest of the files to a temporary directory
+        log.info("Writing patched files to tmpdir")
         temp_dir = Path(tempfile.mkdtemp())
         temp_module_dir = temp_dir / module
         temp_module_dir.mkdir(parents=True, exist_ok=True)
+
         for file, new_content in new_files.items():
             fn = temp_module_dir / file
             with open(fn, "w") as fh:
                 fh.writelines(new_content)
 
+        # copy old files to the temp dir
+        for file in unpatched_module_files:
+            if file.is_file():
+                shutil.copy(file, temp_module_dir / file.relative_to(module_dir))
+            else:
+                shutil.copytree(file, temp_module_dir / file.relative_to(module_dir))
+
         return temp_module_dir
 
     def repo_present(self, repo_name):