This is a standalone tool that creates CWL-abstract descriptions of Galaxy workflow runs or Galaxy workflow files (static files).
This library is easiest to install using pip:
pip install galaxy2cwl
If you want to install manually from this code base, then try:
pip3 install .
or, assuming all dependencies are installed:
python setup.py install
This should install cwl2galaxy
on your PATH.
Alternatively you can run python3 galaxy2cwl/get_cwl_interface.py
directly.
galaxy2cwl INPUT_GALAXY_WORKFLOW(.ga/.yaml) > OUTPUT_WORKFLOW.cwl
A simple workflow to use as example can be found in https://usegalaxy.eu/u/igegu/w/simple-workflow
This workflow is available in different formats in the examples/ directory of the source repository.
examples/simple_workflow_galaxy.ga
examples/simple_workflow_format2_yaml_wrapped.json
examples/simple_workflow_format2.yaml
examples/simple_workflow_cwl-interface.cwl
The objects created with this project are aimed to be part of workflow based RO-Crate packages for registering in WorkflowHub.
WorkflowHub is a project under development that aims at, among other things, serve as a repository for workflows standardizing the metadata description.
As such it provides the possibility of registering workflows in a diverse set of formats and packaging them in a RO-Crate package.
All examples included in this project are readily available in https://dev.workflowhub.eu/
Contributions welcome! Raise pull requests, issues etc on https://github.com/workflowhub-eu/galaxy2cwl/.
Submitted patches are assumed to be licensed under the same BSD 3-Clause license.
Distributed under a BSD 3-Clause license.