nf_core.params_file

Create a YAML parameter file

classnf_core.pipelines.params_file.ParamsFileBuilder(pipeline=None, revision=None)

Bases: object

Class to hold config option to launch a pipeline.

• Parameters:
  • pipeline (str , optional) – Path to a local pipeline path or a remote pipeline.
  • revision (str , optional) – Revision of the pipeline to use.

format_group(definition, show_hidden=False) → str

Format a group of parameters of the schema as commented YAML.

• Parameters:
  • definition (dict) – Definition of the group from the schema
  • show_hidden (bool) – Whether to include hidden parameters
• Returns: Formatted output for a group
• Return type: str

format_param(name: str, properties: Dict, required_properties: List[str] = [], show_hidden: bool = False) → str | None

Format a single parameter of the schema as commented YAML

• Parameters:
  • name (str) – Name of the parameter
  • properties (dict) – Properties of the parameter
  • required_properties (list) – List of required properties
  • show_hidden (bool) – Whether to include hidden parameters
• Returns: Section of a params-file.yml for given parameter None: If the parameter is skipped because it is hidden and show_hidden is not set
• Return type: str

generate_params_file(show_hidden: bool = False) → str

Generate the contents of a parameter template file.

Assumes the pipeline has been fetched (if remote) and the schema loaded.

• Parameters: show_hidden (bool) – Whether to include hidden parameters
• Returns: Formatted output for the pipeline schema
• Return type: str

get_pipeline() → bool | None

Prompt the user for a pipeline name and get the schema

write_params_file(output_fn: Path = PosixPath('nf-params.yaml'), show_hidden=False, force=False) → bool

Build a template file for the pipeline schema.

• Parameters:
  • output_fn (str , optional) – Filename to write the template to.
  • show_hidden (bool , optional) – Include parameters marked as hidden in the output
  • force (bool , optional) – Whether to overwrite existing output file.
• Returns: True if the template was written successfully, False otherwise
• Return type: bool

nf_core.pipelines.params_file._print_wrapped(text, fill_char='-', mode='both', width=80, indent=0, drop_whitespace=True) → str

Helper function to format text for the params-file template.

• Parameters:
  • text (str) – Text to print
  • fill_char (str , optional) – Character to use for creating dividers. Defaults to ‘-‘.
  • mode (str , optional) – Where to place dividers. Defaults to “both”.
  • width (int , optional) – Maximum line-width of the output text. Defaults to 80.
  • indent (int , optional) – Number of spaces to indent the text. Defaults to 0.
  • drop_whitespace (bool , optional) – Whether to drop whitespace from the start and end of lines.