write proper path and raise a UserWarning to avoid printing the error trace

Author: mirpedrol

nf_core/synced_repo.py

@@ -261,11 +261,11 @@ def checkout(self, commit):
                 self.repo.git.checkout(self.branch, force=True)
             else:
                 log.error(
-                    f"Could not check out commit '{commit}' in '{self.remote_url}'.\n"
-                    "To solve this, you can try to remove the cloned rempository and run the command again."
-                    f"This repository is tipically found at `~/.config/nfcore/{self.local_repo_dir}`"
+                    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 e
+                raise UserWarning
 
     def component_exists(self, component_name, component_type, checkout=True, commit=None):
         """
@@ -400,8 +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