Merge pull request #2123 from mirpedrol/dashed-name

only check pipeline name without dashes if the name is provided by prompt

CHANGELOG.md

@@ -16,6 +16,8 @@
 
 ### General
 
+- Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
+
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 
 - Patch release to fix pipeline sync ([#2110](https://github.com/nf-core/tools/pull/2110))

nf_core/create.py

@@ -173,9 +173,10 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
  and "manifest.name" in config_yml["lint"]["nextflow_config"]
  ):
  return param_dict, skip_paths
- # Check that the pipeline name matches the requirements
- if not re.match(r"^[a-z]+$", param_dict["short_name"]):
- raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
+ if param_dict["prefix"] == "nf-core":
+ # Check that the pipeline name matches the requirements
+ if not re.match(r"^[a-z]+$", param_dict["short_name"]):
+ raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
 
  return param_dict, skip_paths
 

nf_core/sync.py

@@ -252,8 +252,9 @@ def make_template_pipeline(self):
  plain=True,
  ).init_pipeline()
  except Exception as err:
- # If sync fails, remove template_yaml_path before raising error.
- os.remove(self.template_yaml_path)
+ if self.template_yaml_path:
+ # If sync fails, remove template_yaml_path before raising error.
+ os.remove(self.template_yaml_path)
  # Reset to where you were to prevent git getting messed up.
  self.repo.git.reset("--hard")
  raise SyncException(f"Failed to rebuild pipeline from template with error:\n{err}")