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__