phc-notebook-tools

Run a notebook as a workflow.

Development

Install PDM and then do

$ pdm install

Running

To run the development version from the root of the source directory do this:

$ cd sandbox
$ python ../phcnb workflow test.ipynb > output.cwl
$ pdm run cwltool --no-read-only --no-match-user output.cwl inputs.yml

The results will be written to output.ipynb and output.txt.