only check out as much of the repo as needed

nf_core/modules/modules_repo.py

@@ -120,7 +120,7 @@ def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False):
  )
  with pbar:
  self.repo.remotes.origin.fetch(
- progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Pulling")
+ depth=1, progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Pulling")
  )
  ModulesRepo.update_local_repo_status(self.fullname, True)
 

nf_core/synced_repo.py

@@ -208,7 +208,7 @@ def checkout_branch(self):
  """
  # only checkout if we're on a detached head or if we're not already on the branch
  if self.repo.head.is_detached or self.repo.active_branch.name != self.branch:
- self.repo.git.checkout(self.branch)
+ self.repo.git.switch(self.branch)
 
  def checkout(self, commit):
  """
@@ -348,7 +348,17 @@ def sha_exists_on_branch(self, sha):
  Verifies that a given commit sha exists on the branch
  """
  self.checkout_branch()
- return sha in (commit.hexsha for commit in self.repo.iter_commits())
+
+ # check if sha exist, if not try shallow fetch until sha
+ sha_exists = False
+ try:
+ self.repo.remotes.origin.fetch(sha, depth=1)
+ sha_exists = True
+ except GitCommandError:
+ log.debug(f"Could not fetch commit {sha} from {self.remote_url}")
+ sha_exists = False
+
+ return sha_exists
 
  def get_commit_info(self, sha):
  """