Create a YAML parameter file

classnf_core.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)

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, properties, required_properties=(), show_hidden=False)

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 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


Prompt the user for a pipeline name and get the schema

write_params_file(output_fn='nf-params.yaml', show_hidden=False, force=False)

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

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.