Merge pull request #2037 from mirpedrol/update-config

Check structure of update entry in .nf-core.yml

CHANGELOG.md

@@ -13,6 +13,8 @@
 
 ### Linting
 
+- Don't lint pipeline name if `manifest.name` in `.nf-core.yml` ([#2035](https://github.com/nf-core/tools/pull/2035))
+
 ### General
 
 - Refactor CLI flag `--hide-progress` to be at the top-level group, like `--verbose` ([#2016](https://github.com/nf-core/tools/pull/2016))

nf_core/components/update.py

@@ -146,6 +146,9 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
         exit_value = True
         all_patches_successful = True
         for modules_repo, component, sha, patch_relpath in components_info:
+            if component is None:
+                # The entry from .nf-core.yml is set to false, skip update of this component
+                continue
             component_fullname = str(Path(self.component_type, modules_repo.repo_path, component))
             # Are we updating the files in place or not?
             dry_run = self.show_diff or self.save_diff_fn
@@ -378,6 +381,19 @@ def get_single_component_info(self, component):
 
         sha = self.sha
         config_entry = None
+        if any(
+            [
+                entry.count("/") == 1
+                and (entry.endswith("modules") or entry.endswith("subworkflows"))
+                and not (entry.endswith(".git") or entry.endswith(".git/"))
+                for entry in self.update_config.keys()
+            ]
+        ):
+            raise UserWarning(
+                "Your '.nf-core.yml' file format is outdated. "
+                "The format should be of the form:\n"
+                "update:\n  <repo_url>:\n    <component_install_directory>:\n      <component_name>:"
+            )
         if isinstance(self.update_config.get(self.modules_repo.remote_url, {}), str):
             # If the repo entry is a string, it's the sha to update to
             config_entry = self.update_config.get(self.modules_repo.remote_url, {})
@@ -386,12 +402,13 @@ def get_single_component_info(self, component):
             config_entry = self.update_config[self.modules_repo.remote_url][install_dir].get(component)
         if config_entry is not None and config_entry is not True:
             if config_entry is False:
-                raise UserWarning(
-                    f"{self.component_type[:-1].title()}'s update entry in '.nf-core.yml' is set to False"
+                log.warn(
+                    f"{self.component_type[:-1].title()}'s update entry in '.nf-core.yml' for '{component}' is set to False"
                 )
+                return (self.modules_repo, None, None, None)
             if not isinstance(config_entry, str):
                 raise UserWarning(
-                    f"{self.component_type[:-1].title()}'s update entry in '.nf-core.yml' is of wrong type"
+                    f"{self.component_type[:-1].title()}'s update entry in '.nf-core.yml' for '{component}' is of wrong type"
                 )
 
             sha = config_entry

nf_core/create.py

@@ -166,10 +166,16 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
         param_dict["logo_dark"] = f"{param_dict['name_noslash']}_logo_dark.png"
         param_dict["version"] = version
 
+        config_yml = nf_core.utils.load_tools_config()
+        if (
+            "lint" in config_yml
+            and "nextflow_config" in config_yml["lint"]
+            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"]):
-            log.error("[red]Invalid workflow name: must be lowercase without punctuation.")
-            sys.exit(1)
+            raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
 
         return param_dict, skip_paths