https://github.com/common-workflow-lab/ipython2cwl

IPython2CWL is a tool for converting IPython Jupyter Notebooks to CWL Command Line Tools by simply providing typing annotation.
https://github.com/common-workflow-lab/ipython2cwl

common-workflow-language cwl docker jupyter jupyter-notebook

Last synced: about 1 month ago
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IPython2CWL is a tool for converting IPython Jupyter Notebooks to CWL Command Line Tools by simply providing typing annotation.

• Host: GitHub
• URL: https://github.com/common-workflow-lab/ipython2cwl
• Owner: common-workflow-lab
• License: apache-2.0
• Created: 2020-06-16T19:27:47.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2025-10-06T07:45:06.000Z (5 months ago)
• Last Synced: 2025-10-06T09:38:35.272Z (5 months ago)
• Topics: common-workflow-language, cwl, docker, jupyter, jupyter-notebook
• Language: Python
• Homepage: https://ipython2cwl.readthedocs.io/
• Size: 335 KB
• Stars: 17
• Watchers: 5
• Forks: 6
• Open Issues: 8
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# IPython2CWL

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IPython2CWL is a tool for converting [IPython](https://ipython.org/) Jupyter Notebooks to

[CWL (Common Workflow Language)](https://www.commonwl.org/) Command Line Tools by simply providing typing annotation.

```python

from ipython2cwl.iotypes import CWLFilePathInput, CWLFilePathOutput

import csv

input_filename: 'CWLFilePathInput' = 'data.csv'

with open(input_filename) as f:

    csv_reader = csv.reader(f)

    data = [line for line in csv_reader]

number_of_lines = len(data)

result_file: 'CWLFilePathOutput' = 'number_of_lines.txt'

with open(result_file, 'w') as f:

    f.write(str(number_of_lines))

```

IPython2CWL is based on [repo2docker](https://github.com/jupyter/repo2docker), the same tool

used by [mybinder](https://mybinder.org/). Now, by writing Jupyter Notebook and publishing them, including repo2docker

configuration, the community can not only execute the notebooks remotely but also to use them as steps in scientific

workflows.

## Install

```

pip install ipython2cwl

```

### Example

```

jupyter repo2cwl https://github.com/giannisdoukas/cwl-annotated-jupyter-notebook.git -o .

```

### Docs

[https://ipython2cwl.readthedocs.io/](https://ipython2cwl.readthedocs.io/en/latest/)

### Demo

[https://github.com/giannisdoukas/ipython2cwl-demo](https://github.com/giannisdoukas/ipython2cwl-demo)