cwl_utils.parser.utils
CWL parser utility functions.
Module Contents
Functions
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Convert stdin, stdout and stderr type shortcuts to files. |
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Load a CWL input file from a URI or a path. |
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Load a CWL input file from a serialized YAML string or a YAML object. |
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Load a CWL input file from a serialized YAML string. |
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Load a CWL input file from a YAML object. |
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Check if all source and sink types of a workflow are compatible before run time. |
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Determine the type for the given sourcenames. |
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Determine the type for the given step output. |
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Determine the type for the given step output. |
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- cwl_utils.parser.utils.convert_stdstreams_to_files(process)
Convert stdin, stdout and stderr type shortcuts to files.
- Parameters:
process (cwl_utils.parser.Process) –
- Return type:
None
- cwl_utils.parser.utils.load_inputfile_by_uri(version, path, loadingOptions=None)
Load a CWL input file from a URI or a path.
- Parameters:
version (str) –
path (Union[str, pathlib.Path]) –
loadingOptions (Optional[cwl_utils.parser.LoadingOptions]) –
- Return type:
Any
- cwl_utils.parser.utils.load_inputfile(version, doc, baseuri=None, loadingOptions=None)
Load a CWL input file from a serialized YAML string or a YAML object.
- cwl_utils.parser.utils.load_inputfile_by_string(version, string, uri, loadingOptions=None)
Load a CWL input file from a serialized YAML string.
- cwl_utils.parser.utils.load_inputfile_by_yaml(version, yaml, uri, loadingOptions=None)
Load a CWL input file from a YAML object.
- cwl_utils.parser.utils.load_step(step)
- Parameters:
step (cwl_utils.parser.WorkflowStep) –
- Return type:
cwl_utils.parser.Process
- cwl_utils.parser.utils.static_checker(workflow)
Check if all source and sink types of a workflow are compatible before run time.
- Parameters:
workflow (cwl_utils.parser.Workflow) –
- Return type:
None
- cwl_utils.parser.utils.type_for_source(process, sourcenames, parent=None, linkMerge=None, pickValue=None)
Determine the type for the given sourcenames.
- cwl_utils.parser.utils.type_for_step_input(step, in_, cwlVersion)
Determine the type for the given step output.
- Parameters:
step (cwl_utils.parser.WorkflowStep) –
in_ (cwl_utils.parser.WorkflowStepInput) –
cwlVersion (str) –
- Return type:
Any
- cwl_utils.parser.utils.type_for_step_output(step, sourcename, cwlVersion)
Determine the type for the given step output.
- cwl_utils.parser.utils.param_for_source_id(process, sourcenames, parent=None, scatter_context=None)
- Parameters:
- Return type:
Union[Union[List[cwl_utils.parser.cwl_v1_0.InputParameter], cwl_utils.parser.cwl_v1_0.InputParameter], Union[List[cwl_utils.parser.cwl_v1_1.WorkflowInputParameter], cwl_utils.parser.cwl_v1_1.WorkflowInputParameter], Union[List[cwl_utils.parser.cwl_v1_2.WorkflowInputParameter], cwl_utils.parser.cwl_v1_2.WorkflowInputParameter]]