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).

Installing

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.

Usage

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 common-workflow-language/common-workflow-language#337 and common-workflow-language/cwl-v1.2#3). As the CWL support in Galaxy increases then conversion could come up with a full CWL workflow file.

Examples

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 examples/simple_workflow_galaxy.ga
• The format2 version yaml wrapped in json can be found in examples/simple_workflow_format2_yaml_wrapped.json
• The format2 pure yaml in examples/simple_workflow_format2.yaml
• The resulting CWL-interface can be found in examples/simple_workflow_cwl-interface.cwl

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/

Contribute

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.

License

• Copyright © 2019-2020, Ignacio Eguinoa, VIB, Universiteit Gent, and workflowhub.eu contributors

Distributed under a BSD 3-Clause license.