nf_core.pipelines.launch

Launch a pipeline, interactively collecting params

classnf_core.pipelines.launch.Launch(pipeline=None, revision=None, command_only=False, params_in=None, params_out=None, save_all=False, show_hidden=False, url=None, web_id=None)

Bases: object

Class to hold config option to launch a pipeline

build_command()

Build the nextflow run command based on what we know

get_pipeline_schema()

Load and validate the schema from the supplied pipeline

get_web_launch_response()

Given a URL for a web-gui launch response, recursively query it until results are ready.

launch_pipeline()

launch_web_gui()

Send schema to nf-core website and launch input GUI

launch_workflow()

Launch nextflow if required

merge_nxf_flag_schema()

Take the Nextflow flag schema and merge it with the pipeline schema

prompt_group(group_id, group_obj)

Prompt for edits to a group of parameters (subschema in ‘definitions’)

  • Parameters:
    • group_id – Parameter ID (string)
    • group_obj – JSON Schema keys (dict)
  • Returns: val answers
  • Return type: Dict of param_id

prompt_param(param_id, param_obj, is_required, answers)

Prompt for a single parameter

prompt_schema()

Go through the pipeline schema and prompt user to change defaults

prompt_web_gui()

Ask whether to use the web-based or cli wizard to collect params

sanitise_web_response()

The web builder returns everything as strings. Use the functions defined in the cli wizard to convert to the correct types.

set_schema_inputs()

Take the loaded schema and set the defaults as the input parameters If a nf_params.json file is supplied, apply these over the top

single_param_to_questionary(param_id, param_obj, answers=None, print_help=True)

Convert a JSONSchema param to a Questionary question

  • Parameters:
    • param_id – Parameter ID (string)
    • param_obj – JSON Schema keys (dict)
    • answers – Optional preexisting answers (dict)
    • print_help – If description and help_text should be printed (bool)
  • Returns: Single Questionary dict, to be appended to questions list

strip_default_params()

Strip parameters if they have not changed from the default
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