nf_core.pipelines.schema

Code to deal with pipeline JSON Schema

classnf_core.pipelines.schema.PipelineSchema

Bases: object

Class to generate a schema object with functions to handle pipeline JSON Schema

_update_validation_plugin_from_config() → None

add_schema_found_configs()

Add anything that’s found in the Nextflow params that’s missing in the pipeline schema Update defaults if they have changed

build_schema(pipeline_dir, no_prompts, web_only, url)

Interactively build a new pipeline schema for a pipeline

build_schema_param(p_val)

Build a pipeline schema dictionary for an param interactively

check_for_input_mimetype()

Check that the input parameter has a mimetype

Common mime types: https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_types/Common_types

  • Returns: The mimetype of the input parameter
  • Return type: mimetype (str)
  • Raises: LookupError – If the input parameter is not found or defined in the correct place

del_schema_filename() → None

get_schema_defaults() → None

Generate set of default input parameters from schema.

Saves defaults to self.schema_defaults Returns count of how many parameters were found (with or without a default value)

get_schema_filename() → str

get_schema_path(path: str | Path, local_only: bool = False, revision: str | None = None) → None

Given a pipeline name, directory, or path, set self.schema_filename

get_schema_types() → None

Get a list of all parameter types in the schema

get_web_builder_response()

Given a URL for a Schema build response, recursively query it until results are ready. Once ready, validate Schema and write to disk.

get_wf_params()

Load the pipeline parameter defaults using nextflow config Strip out only the params. values and ignore anything that is not a flat variable

launch_web_builder()

Send pipeline schema to web builder and wait for response

load_input_params(params_path)

Load a given a path to a parameters file (JSON/YAML)

These should be input parameters used to run a pipeline with the Nextflow -params-file option.

load_lint_schema()

Load and lint a given schema to see if it looks valid

load_schema()

Load a pipeline schema from a file

make_skeleton_schema()

Make a new pipeline schema from the template

markdown_param_table(properties, required, columns)

Creates a markdown table for params from jsonschema properties section

  • Parameters:
    • properties (dict) – A jsonschema properties dictionary
    • required (list) – A list of the required fields. Should come from the same level of the jsonschema as properties
    • columns (list) – A list of columns to write
  • Returns: A string with the markdown table
  • Return type: str

markdown_to_html(markdown_str)

Convert markdown to html

Prints documentation for the schema.

prompt_remove_schema_notfound_config(p_key)

Check if a given key is found in the nextflow config params and prompt to remove it if note

Returns True if it should be removed, False if not.

remove_schema_empty_definitions()

Go through top-level schema remove definitions that don’t have any property attributes

remove_schema_notfound_configs()

Go through top-level schema and all definitions sub-schemas to remove anything that’s not in the nextflow config.

remove_schema_notfound_configs_single_schema(schema)

Go through a single schema / set of properties and strip out anything that’s not in the nextflow config.

Takes: Schema or sub-schema with properties key Returns: Cleaned schema / sub-schema

sanitise_param_default(param)

Given a param, ensure that the default value is the correct variable type

save_schema(suppress_logging=False)

Save a pipeline schema to a file

propertyschema_filename: str

schema_to_markdown(columns)

Creates documentation for the schema in Markdown format.

set_schema_filename(schema: str) → None

validate_config_default_parameter(param, schema_param, config_default)

Assure that default parameters in the nextflow.config are correctly set by comparing them to their type in the schema

validate_default_params()

Check that all default parameters in the schema are valid Ignores ‘required’ flag, as required parameters might have no defaults

Additional check that all parameters have defaults in nextflow.config and that these are valid and adhere to guidelines

validate_params()

Check given parameters against a schema and validate

validate_schema(schema=None)

Check that the Schema is valid

Returns: Number of parameters found

validate_schema_title_description(schema=None)

Extra validation command for linting. Checks that the schema “$id”, “title” and “description” attributes match the pipeline config.
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