Merge pull request #3213 from mirpedrol/fix-params-validation

Linting: Fix bug when linting schema params

nf_core/pipelines/lint/nextflow_config.py

@@ -465,6 +465,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
                     f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
                 )
         else:
+            schema_default = str(schema.schema_defaults[param_name])
             failed.append(
                 f"Default value from the Nextflow schema `{param} = {self._wrap_quotes(schema_default)}` not found in `nextflow.config`."
             )

nf_core/pipelines/schema.py

@@ -97,11 +97,16 @@ def _update_validation_plugin_from_config(self) -> None:
                 conf.get("validation.help.fullParameter", "helpFull"),
                 conf.get("validation.help.showHiddenParameter", "showHidden"),
             ]  # Help parameter should be ignored by default
-            ignored_params_config = conf.get("validation.defaultIgnoreParams", [])
+            ignored_params_config_str = conf.get("validation.defaultIgnoreParams", "")
+            ignored_params_config = [
+                item.strip().strip("'") for item in ignored_params_config_str[1:-1].split(",")
+            ]  # Extract list elements and remove whitespace
+
             if len(ignored_params_config) > 0:
                 log.debug(f"Ignoring parameters from config: {ignored_params_config}")
                 ignored_params.extend(ignored_params_config)
             self.ignored_params = ignored_params
+            log.debug(f"Ignoring parameters: {self.ignored_params}")
             self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
 
         else: