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}")