General: Add hint to solve git errors with a synced repo

CHANGELOG.md

@@ -38,6 +38,7 @@
 - handle new schema structure in `nf-core pipelines create-params-file` ([#3276](https://github.com/nf-core/tools/pull/3276))
 - Update Gitpod image to use Miniforge instead of Miniconda([#3274](https://github.com/nf-core/tools/pull/3274))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3 ([#3275](https://github.com/nf-core/tools/pull/3275))
+- Add hint to solve git errors with a synced repo ([#3279](https://github.com/nf-core/tools/pull/3279))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

nf_core/synced_repo.py

@@ -260,7 +260,12 @@ def checkout(self, commit):
                 log.debug(f"Overwriting local changes in '{self.local_repo_dir}'")
                 self.repo.git.checkout(self.branch, force=True)
             else:
-                raise e
+                log.error(
+                    f"You found a git error: {e}\n"
+                    "To solve this, you can try to remove the cloned rempository and run the command again.\n"
+                    f"This repository is typically found at `{self.local_repo_dir}`"
+                )
+                raise UserWarning
 
     def component_exists(self, component_name, component_type, checkout=True, commit=None):
         """
@@ -395,8 +400,16 @@ def get_component_git_log(
             old_component_path = Path("modules", component_name)
             commits_old_iter = self.repo.iter_commits(max_count=depth, paths=old_component_path)
 
-        commits_old = [{"git_sha": commit.hexsha, "trunc_message": commit.message} for commit in commits_old_iter]
-        commits_new = [{"git_sha": commit.hexsha, "trunc_message": commit.message} for commit in commits_new_iter]
+        try:
+            commits_old = [{"git_sha": commit.hexsha, "trunc_message": commit.message} for commit in commits_old_iter]
+            commits_new = [{"git_sha": commit.hexsha, "trunc_message": commit.message} for commit in commits_new_iter]
+        except git.GitCommandError as e:
+            log.error(
+                f"You found a git error: {e}\n"
+                "To solve this, you can try to remove the cloned rempository and run the command again.\n"
+                f"This repository is typically found at `{self.local_repo_dir}`"
+            )
+            raise UserWarning
         commits = iter(commits_new + commits_old)
 
         return commits