cwltool.workflow

Module Contents

Classes

Workflow	Abstract CWL Process.
WorkflowStep	Abstract CWL Process.

Functions

default_make_tool(toolpath_object, loadingContext)	Instantiate the given CWL Process.
used_by_step(step, shortinputid)

cwltool.workflow.default_make_tool(toolpath_object, loadingContext)

Instantiate the given CWL Process.

Parameters:

• toolpath_object (ruamel.yaml.comments.CommentedMap)

• loadingContext (cwltool.context.LoadingContext)

Return type:

cwltool.process.Process

class cwltool.workflow.Workflow(toolpath_object, loadingContext)

Bases: cwltool.process.Process

Abstract CWL Process.

Parameters:

• toolpath_object (ruamel.yaml.comments.CommentedMap)

• loadingContext (cwltool.context.LoadingContext)

make_workflow_step(toolpath_object, pos, loadingContext, parentworkflowProv=None)

Parameters:

• toolpath_object (ruamel.yaml.comments.CommentedMap)

• pos (int)

• loadingContext (cwltool.context.LoadingContext)

• parentworkflowProv (Optional[cwltool.cwlprov.provenance_profile.ProvenanceProfile])

Return type:

WorkflowStep

job(job_order, output_callbacks, runtimeContext)

Parameters:

• job_order (cwltool.utils.CWLObjectType)

• output_callbacks (Optional[cwltool.utils.OutputCallbackType])

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

visit(op)

Parameters:

op (Callable[[ruamel.yaml.comments.CommentedMap], None])

Return type:

None

cwltool.workflow.used_by_step(step, shortinputid)

Parameters:

• step (cwltool.utils.StepType)

• shortinputid (str)

Return type:

bool

class cwltool.workflow.WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv=None)

Bases: cwltool.process.Process

Abstract CWL Process.

Parameters:

• toolpath_object (ruamel.yaml.comments.CommentedMap)

• pos (int)

• loadingContext (cwltool.context.LoadingContext)

• parentworkflowProv (Optional[cwltool.cwlprov.provenance_profile.ProvenanceProfile])

checkRequirements(rec, supported_process_requirements)

Check the presence of unsupported requirements.

Parameters:

• rec (Union[MutableSequence[cwltool.utils.CWLObjectType], cwltool.utils.CWLObjectType, cwltool.utils.CWLOutputType, None])

• supported_process_requirements (Iterable[str])

Return type:

None

receive_output(output_callback, jobout, processStatus)

Parameters:

• output_callback (cwltool.utils.OutputCallbackType)

• jobout (cwltool.utils.CWLObjectType)

• processStatus (str)

Return type:

None

job(job_order, output_callbacks, runtimeContext)

Initialize sub-workflow as a step in the parent profile.

Parameters:

• job_order (cwltool.utils.CWLObjectType)

• output_callbacks (Optional[cwltool.utils.OutputCallbackType])

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

visit(op)

Parameters:

op (Callable[[ruamel.yaml.comments.CommentedMap], None])

Return type:

None