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https://github.com/workflowhub-eu/galaxy2cwl

Standalone version tool to get cwl descriptions (initially an abstract cwl interface) of galaxy workflows and Galaxy workflows executions.
https://github.com/workflowhub-eu/galaxy2cwl

biohackcovid20 cwl galaxy galaxy-workflows ro-crate workflow workflowhub

Last synced: 3 months ago
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Standalone version tool to get cwl descriptions (initially an abstract cwl interface) of galaxy workflows and Galaxy workflows executions.

Host: GitHub
URL: https://github.com/workflowhub-eu/galaxy2cwl
Owner: workflowhub-eu
License: bsd-3-clause
Created: 2019-07-07T15:59:13.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2022-03-24T08:12:42.000Z (almost 3 years ago)
Last Synced: 2024-10-15T00:15:56.571Z (3 months ago)
Topics: biohackcovid20, cwl, galaxy, galaxy-workflows, ro-crate, workflow, workflowhub
Language: Python
Homepage:
Size: 96.7 KB
Stars: 4
Watchers: 3
Forks: 5
Open Issues: 9
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

[![PyPI version](https://badge.fury.io/py/galaxy2cwl.svg)](https://pypi.org/project/galaxy2cwl/)

# 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 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.

## Examples
A simple workflow to use as example can be found in

This workflow is available in different formats in the [examples/ directory](https://github.com/workflowhub-eu/galaxy2cwl/tree/master/examples) 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](https://github.com/workflowhub-eu/about/wiki/Workflow-RO-Crate) packages for registering in _WorkflowHub_.

[WorkflowHub](https://about.workflowhub.eu/) 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

## Contribute

Contributions welcome! Raise pull requests, issues etc on .

Submitted patches are assumed to be licensed under the same BSD 3-Clause license.

## License

Distributed under a [BSD 3-Clause license](https://github.com/workflowhub-eu/cwl-from-galaxy/blob/master/LICENSE).