cwltool.workflow_job

Module Contents

Classes

WorkflowJobStep

Generated for each step in Workflow.steps().

ReceiveScatterOutput

Produced by the scatter generators.

WorkflowJob

Generates steps from the Workflow.

Functions

parallel_steps(steps, rc, runtimeContext)

nested_crossproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)

crossproduct_size(joborder, scatter_keys)

flat_crossproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)

dotproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)

match_types(sinktype, src, iid, inputobj, linkMerge, valueFrom)

object_from_state(state, params, frag_only, supportsMultipleInput, sourceField, incomplete = False)

class cwltool.workflow_job.WorkflowJobStep(step)

Generated for each step in Workflow.steps().

Parameters

step (cwltool.workflow.WorkflowStep) –

job(self, joborder, output_callback, runtimeContext)
Parameters

  • joborder (cwltool.utils.CWLObjectType) –

  • output_callback (Optional[cwltool.utils.OutputCallbackType]) –

  • runtimeContext (cwltool.context.RuntimeContext) –

Return type

cwltool.utils.JobsGeneratorType

class cwltool.workflow_job.ReceiveScatterOutput(output_callback, dest, total)

Produced by the scatter generators.

Parameters

  • output_callback (cwltool.utils.ScatterOutputCallbackType) –

  • dest (cwltool.utils.ScatterDestinationsType) –

  • total (int) –

receive_scatter_output(self, index, jobout, processStatus)
Parameters

  • index (int) –

  • jobout (cwltool.utils.CWLObjectType) –

  • processStatus (str) –

Return type

None

setTotal(self, total, steps)

Set the total number of expected outputs along with the steps.

This is necessary to finish the setup.

Parameters

  • total (int) –

  • steps (List[Optional[cwltool.utils.JobsGeneratorType]]) –

Return type

None

cwltool.workflow_job.parallel_steps(steps, rc, runtimeContext)
Parameters
Return type

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.nested_crossproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)
Parameters

  • process (WorkflowJobStep) –

  • joborder (cwltool.utils.CWLObjectType) –

  • scatter_keys (MutableSequence[str]) –

  • output_callback (cwltool.utils.ScatterOutputCallbackType) –

  • runtimeContext (cwltool.context.RuntimeContext) –

Return type

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.crossproduct_size(joborder, scatter_keys)
Parameters

  • joborder (cwltool.utils.CWLObjectType) –

  • scatter_keys (MutableSequence[str]) –

Return type

int

cwltool.workflow_job.flat_crossproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)
Parameters

  • process (WorkflowJobStep) –

  • joborder (cwltool.utils.CWLObjectType) –

  • scatter_keys (MutableSequence[str]) –

  • output_callback (cwltool.utils.ScatterOutputCallbackType) –

  • runtimeContext (cwltool.context.RuntimeContext) –

Return type

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.dotproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)
Parameters

  • process (WorkflowJobStep) –

  • joborder (cwltool.utils.CWLObjectType) –

  • scatter_keys (MutableSequence[str]) –

  • output_callback (cwltool.utils.ScatterOutputCallbackType) –

  • runtimeContext (cwltool.context.RuntimeContext) –

Return type

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.match_types(sinktype, src, iid, inputobj, linkMerge, valueFrom)
Parameters

  • sinktype (Optional[cwltool.utils.SinkType]) –

  • src (cwltool.utils.WorkflowStateItem) –

  • iid (str) –

  • inputobj (cwltool.utils.CWLObjectType) –

  • linkMerge (Optional[str]) –

  • valueFrom (Optional[str]) –

Return type

bool

cwltool.workflow_job.object_from_state(state, params, frag_only, supportsMultipleInput, sourceField, incomplete=False)
Parameters

  • state (Dict[str, Optional[cwltool.utils.WorkflowStateItem]]) –

  • params (cwltool.utils.ParametersType) –

  • frag_only (bool) –

  • supportsMultipleInput (bool) –

  • sourceField (str) –

  • incomplete (bool) –

Return type

Optional[cwltool.utils.CWLObjectType]

class cwltool.workflow_job.WorkflowJob(workflow, runtimeContext)

Generates steps from the Workflow.

Parameters
do_output_callback(self, final_output_callback)
Parameters

final_output_callback (cwltool.utils.OutputCallbackType) –

Return type

None

receive_output(self, step, outputparms, final_output_callback, jobout, processStatus)
Parameters

  • step (WorkflowJobStep) –

  • outputparms (List[cwltool.utils.CWLObjectType]) –

  • final_output_callback (cwltool.utils.OutputCallbackType) –

  • jobout (cwltool.utils.CWLObjectType) –

  • processStatus (str) –

Return type

None

try_make_job(self, step, final_output_callback, runtimeContext)
Parameters
Return type

cwltool.utils.JobsGeneratorType

run(self, runtimeContext, tmpdir_lock=None)

Log the start of each workflow.

Parameters
Return type

None

job(self, joborder, output_callback, runtimeContext)
Parameters

  • joborder (cwltool.utils.CWLObjectType) –

  • output_callback (Optional[cwltool.utils.OutputCallbackType]) –

  • runtimeContext (cwltool.context.RuntimeContext) –

Return type

cwltool.utils.JobsGeneratorType