AiiDA plugin turning AiiDA into a Common Worfklow Language (CWL) engine.
This plugin is currently in development and a pre-alpha stage. The plugin does not support the complete Common Workflow Language spec. To get an idea of what functionality is supported, please refer to the examples.
The recommended method of installation is through the pip package installer for Python:
pip install aiida-cwl
To use aiida-cwl, a configured AiiDA profile is required.
The verdi CLI of AiiDA provides a command that attempts to automatically create one:
verdi quicksetup
Please refer to the AiiDA's documentation for more detailed instructions. Once an AiiDA profile is available, there are two ways of running a CWL workflow:
- Application programming interface (API) in Python
- Command line interface (CLI)
The aiida-cwl provides a Python API to run CWL documents.
The aiida_cwl.run function requires the filepath to the workflow definition file and the input parameters.
For example, imagine there is a workflow definition in tool.cwl and the parameters are defined in parameters.yml, the workflow can be run as follows:
import pathlib
from aiida_cwl import run
filepath_document = pathlib.Path('tool.cwl')
filepath_parameters = pathlib.Path('parameters.yml')
results, node = run(filepath_document, filepath_parameters)
assert node.is_finished_ok
print(results['stdout'].get_content())The run function returns a tuple where the first element is a dictionary of the parsed output nodes, and the second element is a ProcessNode which represents the execution of the workflow in AiiDA's provenance graph.
The stdout of the tool is always captured and automatically attached as the stdout output node.
Warning Filepaths in the workflow definition or parameter file are taken to be relative with respect to the current working directory when the workflow is executed.
The aiida-cwl package ships with the likely named CLI aiida-cwl.
It is a small wrapper around the Python API.
To run a CWL workflow, simply pass its filepath, as well as that of the parameters file to the aiida-cwl runner command:
aiida-cwl runner tool.cwl parameters.yml
The command will print the status of the executed tool as well as the generated outputs and content of stdout:
Success: ShellJob<echo@localhost><90815> finished successfully.
Results: {
'stderr': <SinglefileData: uuid: a771eaf4-a976-4019-bc4e-37eb9e050b14 (pk: 90818)>,
'stdout': <SinglefileData: uuid: f8736c8e-43c8-4ace-b48c-8e9a410a7949 (pk: 90819)>
}
Stdout: Hello world!
The examples directory of this repository contains various examples of CWL workflows that are supported by aiida-cwl.
The aiida-cwl plugin package is released under the MIT license.
See the LICENSE.txt file for more details.