Handle dirty local module repos by force checkout of commits and branches if needed

CHANGELOG.md

@@ -17,6 +17,7 @@
 - update ruff to 0.2.0 and add it to pre-commit step ([#2725](https://github.com/nf-core/tools/pull/2725))
 - Update codecov/codecov-action digest to e0b68c6 ([#2728](https://github.com/nf-core/tools/pull/2728))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1 ([#2730](https://github.com/nf-core/tools/pull/2730))
+- Force checkout of commits and branches if needed ([#2734](https://github.com/nf-core/tools/pull/2734))
 
 ## [v2.12.1 - Aluminium Wolf - Patch](https://github.com/nf-core/tools/releases/tag/2.12.1) - [2024-02-01]
 

nf_core/synced_repo.py

@@ -208,7 +208,12 @@ def checkout_branch(self):
         """
         Checks out the specified branch of the repository
         """
-        self.repo.git.checkout(self.branch)
+        try:
+            self.repo.git.checkout(self.branch)
+        except GitCommandError as e:
+            if "Your local changes to the following files would be overwritten by checkout" in str(e):
+                log.debug(f"Overwriting local changes in '{self.local_repo_dir}'")
+                self.repo.git.checkout(self.branch, force=True)
 
     def checkout(self, commit):
         """
@@ -217,7 +222,10 @@ def checkout(self, commit):
         Args:
             commit (str): Git SHA of the commit
         """
-        self.repo.git.checkout(commit)
+        try:
+            self.repo.git.checkout(commit)
+        except GitCommandError:
+            self.repo.git.checkout(commit, force=True)
 
     def component_exists(self, component_name, component_type, checkout=True, commit=None):
         """