cwltool.workflow

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)

Module Contents

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)

provenance_object: cwltool.cwlprov.provenance_profile.ProvenanceProfile | None = None

prov_obj

loadingContext

requirements

hints

steps: List[WorkflowStep] = []

validation_errors = []

workflow_inputs

workflow_outputs

step_inputs: List[cwltool.utils.CWLObjectType] = []

step_outputs: List[cwltool.utils.CWLObjectType] = []

param_to_step: Dict[str, cwltool.utils.CWLObjectType]

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 (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])

debug

loadingContext

parent_requirements

requirements

hints

validation_errors = []

bound

missing_values = []

prov_obj: cwltool.cwlprov.provenance_profile.ProvenanceProfile | None = 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 (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