README.md

Workflow implemetation with CWL

The implementation with CWL requires that all the dependencies are provided by the environment. If you have miniconda installed, you can simply create a respective environment by typing

conda env create --file default_env.yml --prefix ./simpleusecase
conda activate ./simpleusecase

Note that by specifying the --prefix option you can simply remove all downloaded packages afterwards by removing the folder given to prefix. To execute the workflow after activating the environment, simply type

cwltool wf_run_use_case.cwl

into your terminal.

Or you can use the conda dependency feature of the CWL reference runner to obtain the dependencies dynamically:

cwltool --beta-conda-dependencies wf_run_use_case.cwl

Note that there exist tools to visualize, edit or create cwl workflows. For instance, you can visualize workflows contained in git repositories with view.commonwl.org, or you can use the Rabix Composer to compose workflows locally on your machine.