nipoppy.workflows.runner.Runner

class nipoppy.workflows.runner.Runner(simulate=False, keep_workdir=False, *args, **kwargs)

Abstract class for workflow runners.

Parameters:

• simulate (bool)

• keep_workdir (bool)

launch_boutiques_run(participant_id, session_id, container_config=None, objs=None, **kwargs)

Launch a pipeline run using Boutiques.

Parameters:

• participant_id (str)

• session_id (str)

• container_config (Optional[nipoppy.config.container.ContainerConfig])

• objs (Optional[list])

process_container_config(participant_id, session_id, bind_paths=None)

Update container config and generate container command.

Parameters:

• participant_id (str)

• session_id (str)

• bind_paths (Optional[list[nipoppy.env.StrOrPathLike]])

Return type:

Tuple[str, nipoppy.config.container.ContainerConfig]

keep_workdir = False

simulate = False