Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Linting: Fix bug when linting schema params #3213

Merged
merged 2 commits into from
Oct 10, 2024
Merged

Linting: Fix bug when linting schema params #3213

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
51bbd46
assign schema_default when a param is found in the schema but not in …
mirpedrol Oct 10, 2024
d4980ca
parse defaultIgnoreParams correctly
mashehu Oct 10, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions nf_core/pipelines/lint/nextflow_config.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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`."
)
Expand Down
7 changes: 6 additions & 1 deletion nf_core/pipelines/schema.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
Loading