cwlkernel repository Module

CWLComponent

class cwlkernel.cwlrepository.CWLComponent.CWLTool(workflow_id: str, command_line_tool: Dict[KT, VT])

command_line_tool

compose_requirements() → Dict[KT, VT]

inputs

outputs

to_dict() → Dict[KT, VT]

to_yaml() → str

class cwlkernel.cwlrepository.CWLComponent.CWLWorkflow(workflow_id: str, workflow: Optional[Dict[KT, VT]] = None)

add(component: cwlkernel.cwlrepository.CWLComponent.WorkflowComponent, step_name: str, run_reference: Optional[str] = None) → None

add_input(workflow_input: Dict[KT, VT], step_id: str, in_step_id: str)

add_output_source(output_ref: str, type_of: str)

add_step_in_out(connect: Union[str, dict], step_in_name: str, step_in: str, step_out: Optional[str] = None, step_out_id: Optional[str] = None)

compose_requirements() → Dict[KT, VT]

inputs

outputs

remove(component: cwlkernel.cwlrepository.CWLComponent.WorkflowComponent) → None

steps

to_dict() → Dict[KT, VT]

to_yaml() → str

validate()

class cwlkernel.cwlrepository.CWLComponent.WorkflowComponent(workflow_id: str, component: Optional[Dict[KT, VT]])

compose_requirements() → Dict[KT, VT]

get_input(input_id: str) → Optional[Dict[KT, VT]]

get_output(output_id: str) → Optional[Dict[KT, VT]]

id

inputs

outputs

to_dict() → Dict[KT, VT]

to_yaml() → str

class cwlkernel.cwlrepository.CWLComponent.WorkflowComponentFactory

get_workflow_component(yaml_string: str) → cwlkernel.cwlrepository.CWLComponent.WorkflowComponent

CWLRepository

exception cwlkernel.cwlrepository.cwlrepository.MissingIdError

class cwlkernel.cwlrepository.cwlrepository.WorkflowRepository(directory: pathlib.Path)

classmethod get_instance() → __SingletonWorkflowRepository__