Job.Runner API

The Runner contains the methods needed to configure and start a Toil run.

class Job.Runner[source]

Used to setup and run Toil workflow.

static getDefaultArgumentParser()[source]

Get argument parser with added toil workflow options.

Return type

ArgumentParser

Returns

The argument parser used by a toil workflow with added Toil options.

static getDefaultOptions(jobStore)[source]

Get default options for a toil workflow.

Parameters

jobStore (str) – A string describing the jobStore for the workflow.

Return type

Namespace

Returns

The options used by a toil workflow.

static addToilOptions(parser)[source]

Adds the default toil options to an optparse or argparse parser object.

Parameters

parser (Union[OptionParser, ArgumentParser]) – Options object to add toil options to.

Return type

None

static startToil(job, options)[source]

Run the toil workflow using the given options.

Deprecated by toil.common.Toil.start.

(see Job.Runner.getDefaultOptions and Job.Runner.addToilOptions) starting with this job. :type job: Job :param job: root job of the workflow :raises: toil.exceptions.FailedJobsException if at the end of function there remain failed jobs. :rtype: Any :return: The return value of the root job’s run function.

Parameters

job (Job) –

Return type

Any