Workflow API classes¶
CWL Workflow¶
Workflow¶
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class
cwlgen.workflow.
Workflow
(workflow_id=None, label=None, doc=None, cwl_version='v1.0', inputs=None, outputs=None, steps=None, requirements=None, hints=None)[source]¶ A workflow describes a set of steps and the dependencies between those steps. When a step produces output that will be consumed by a second step, the first step is a dependency of the second step.
Documentation: https://www.commonwl.org/v1.0/Workflow.html#Workflow
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__init__
(workflow_id=None, label=None, doc=None, cwl_version='v1.0', inputs=None, outputs=None, steps=None, requirements=None, hints=None)[source]¶ Parameters: - workflow_id (STRING) – The unique identifier for this process object.
- label (STRING) – A short, human-readable label of this process object.
- doc (STRING) – A long, human-readable description of this process object.
- cwl_version (CWLVersion) – CWL document version. Always required at the document root. Default: ‘v1.0’
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Inputs and Outputs¶
InputParameter¶
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class
cwlgen.workflow.
InputParameter
(param_id, label=None, secondary_files=None, param_format=None, streamable=None, doc=None, input_binding=None, default=None, param_type=None)[source]¶ Documentation: https://www.commonwl.org/v1.0/Workflow.html#InputParameter
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__init__
(param_id, label=None, secondary_files=None, param_format=None, streamable=None, doc=None, input_binding=None, default=None, param_type=None)[source]¶ Parameters: - param_id (STRING) – unique identifier for this parameter
- label (STRING) – short, human-readable label
- secondary_files (STRING) – If type is a file, describes files that must be included alongside the primary file(s)
- param_format (STRING) – If type is a file, uri to ontology of the format or exact format
- streamable (BOOLEAN) – If type is a file, true indicates that the file is read or written sequentially without seeking
- doc (STRING) – documentation
- param_type (STRING corresponding to CWLType) – type of data assigned to the parameter
- input_binding (CommandLineBinding) –
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WorkflowStep¶
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class
cwlgen.workflow.
WorkflowStep
(step_id, run, label=None, doc=None, scatter=None, scatter_method=None)[source]¶ A workflow step is an executable element of a workflow. It specifies the underlying process implementation (such as CommandLineTool or another Workflow) in the run field and connects the input and output parameters of the underlying process to workflow parameters.
Documentation: https://www.commonwl.org/v1.0/Workflow.html#WorkflowStep
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__init__
(step_id, run, label=None, doc=None, scatter=None, scatter_method=None)[source]¶ Parameters: - step_id (STRING) – The unique identifier for this workflow step.
- run (STRING | CommandLineTool | ExpressionTool | Workflow) – Specifies the process to run.
- label (STRING) – A short, human-readable label of this process object.
- doc (STRING | list[STRING]) – A long, human-readable description of this process object.
- scatter (STRING | list[STRING]) – Field to scatter on, see: https://www.commonwl.org/v1.0/Workflow.html#WorkflowStep
- scatter_method (STRING | list[STRING] in [dotproduct, nested_crossproduct, flat_crossproduct]) – Required if scatter is an array of more than one element.
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