scriptcwl.library module

class scriptcwl.library.StepsLibrary(working_dir=None)

Bases: object

Oject to store steps that can be used to build workflows

get_step(name)

list_steps()

load(steps_dir=None, step_file=None, step_list=None)

scriptcwl.library.load_steps(working_dir=None, steps_dir=None, step_file=None, step_list=None)

Return a dictionary containing Steps read from file.

Args:

steps_dir (str, optional): path to directory containing CWL files. step_file (str, optional): path or http(s) url to a single CWL file. step_list (list, optional): a list of directories, urls or local file

paths to CWL files or directories containing CWL files.

Return:

dict containing (name, Step) entries.

scriptcwl.library.load_yaml(filename)

Return object in yaml file.

scriptcwl.library.name_in_workflow(iri)

Extract the name of a step in a subworkflow.

scriptcwl.library.sort_loading_order(step_files)

Sort step files into correct loading order.

The correct loading order is first tools, then workflows without subworkflows, and then workflows with subworkflows. This order is required to avoid error messages when a working directory is used.