Fix nf-core#1419

CHANGELOG.md

@@ -17,6 +17,7 @@
 - Add an empty line to `modules.json`, `params.json` and `nextflow-schema.json` when dumping them to avoid prettier errors.
 - Add actions workflow to respond to `@nf-core-bot fix linting` comments on nf-core/tools PRs
 - Linting: Don't allow a `.nf-core.yaml` file, should be `.yml` ([#1515](https://github.com/nf-core/tools/pull/1515)).
+- Not all definitions in JSON schema have a "properties", leading to an error ([#1419](https://github.com/nf-core/tools/issues/1419))
 
 ### Modules
 

nf_core/schema.py

@@ -613,6 +613,29 @@ def get_wf_params(self):
  )
  )
 
+ def remove_schema_empty_definitions(self):
+ """
+ Go through top-level schema remove definitions that don't have
+ any property attributes
+ """
+ # Make copy of schema
+ schema_no_empty_definitions = copy.deepcopy(self.schema)
+
+ ## Identify and remove empty definitions from the schema
+ empty_definitions = []
+ for d_key, d_schema in list(schema_no_empty_definitions.get("definitions", {}).items()):
+ if not d_schema['properties']:
+ del schema_no_empty_definitions["definitions"][d_key]
+ empty_definitions.append(d_key)
+
+ # Remove "allOf" group with empty definitions from the schema
+ for d_key in empty_definitions:
+ allOf = {'$ref': "#/definitions/{}".format(d_key)}
+ if allOf in schema_no_empty_definitions["allOf"]:
+ schema_no_empty_definitions["allOf"].remove(allOf)
+
+ self.schema = schema_no_empty_definitions
+
  def remove_schema_notfound_configs(self):
  """
  Go through top-level schema and all definitions sub-schemas to remove
@@ -625,6 +648,8 @@ def remove_schema_notfound_configs(self):
  cleaned_schema, p_removed = self.remove_schema_notfound_configs_single_schema(definition)
  self.schema["definitions"][d_key] = cleaned_schema
  params_removed.extend(p_removed)
+ self.remove_schema_empty_definitions()
+
  return params_removed
 
  def remove_schema_notfound_configs_single_schema(self, schema):