diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index f68c27b2d..3233f6948 100644
--- a/nf_core/modules/modules_json.py
+++ b/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
 
@@ -823,11 +825,12 @@ def try_apply_patch_reverse(self, module, repo_name, patch_relpath, module_dir):
         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
+        # Write the patched files and rest of the files to a temporary directory
         log.debug("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:
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 5c31e9691..23966be13 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -314,15 +314,19 @@ def component_files_identical(self, component_name, base_path, commit, component
             self.checkout_branch()
         else:
             self.checkout(commit)
-        component_files = ["main.nf", "meta.yml"]
-        files_identical = {file: True for file in component_files}
+        files_identical = {}
         component_dir = self.get_component_dir(component_name, component_type)
+        component_files = [file.relative_to(component_dir) for file in Path(component_dir).rglob("*") if file.is_file()]
         for file in component_files:
-            try:
-                files_identical[file] = filecmp.cmp(os.path.join(component_dir, file), os.path.join(base_path, file))
-            except FileNotFoundError:
-                log.debug(f"Could not open file: {os.path.join(component_dir, file)}")
+            component_file = component_dir / file
+            base_file = base_path / file
+            if not base_file.exists():
+                files_identical[file] = False
                 continue
+            try:
+                files_identical[file] = filecmp.cmp(component_file, base_file)
+            except FileNotFoundError as e:
+                raise UserWarning(f"Could not open file: {e.filename}")
         self.checkout_branch()
         return files_identical