Convert a Galaxy workflow to abstract Common Workflow Language (CWL)
Convert Galaxy workflow files to (abstract) CWL
This is a standalone tool that creates CWL-abstract descriptions of Galaxy workflow runs or Galaxy workflow files (static files).
galaxy2cwl INPUT_GALAXY_WORKFLOW(.ga/.yaml) > OUTPUT_WORKFLOW.cwl
- The tool works with inputs in both format1 (json format .ga, currently the standard for Galaxy workflow definitions) and format2. As described in the implementation (https://github.com/galaxyproject/gxformat2), gxformat2 is 'a highly experimental format and will change rapidly in potentially backward incompatible ways until the code is merged into the Galaxy server and enabled by default' therefore the conversion to CWL from this format is also variable and can rapidly change and/or break.
- Initially the output of this project a CWL-abstract definition (aka cwl-interface, see https://github.com/common-workflow-language/common-workflow-language/issues/337 and https://github.com/common-workflow-language/cwl-v1.2/pull/3). As the CWL support in Galaxy increases then conversion could come up with a full CWL workflow file.
- Copyright © 2019-2020, Ignacio Eguinoa, VIB, Universiteit Gent, and workflowhub.eu contributors
Distributed under a BSD 3-Clause license.
Installing from source
Easiest is to use
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.
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.
- The Galaxy .ga format is in
- The format2 version yaml wrapped in json can be found in
- The format2 pure yaml in
- The resulting CWL-interface can be found in
Packaging with RO-Crate
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.
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Hashes for galaxy2cwl-0.1.4-py3-none-any.whl