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Run CWL workflows

The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments.

We use the CWL Calrissian implementation, note that this project is young and still in development, feel free to report issues and contribute to its documentation.

Clone the repository​

  1. Git clone in /calrissian on a persistent volume on the cluster from a terminal. 
cd /data/calrissian
git clone --recursive https://github.com/MaastrichtU-IDS/d2s-project-template.git
cd d2s-project-template
  1. You will need to create the folder for the workflow output data, in our example it is output-data:
mkdir /data/calrissian/output-data
  1. You might need to give permissions (CWL execution will fail due to permissions issues otherwise).
chmod -R 777 /data/calrissian

Start pod​

Start the CWL execution from your computer using the oc client. Define the CWL command arguments to run in run-workflows-cwl.yaml (be careful to properly define the paths to the CWL files in the pod storage).

oc create -f d2s-core/support/run-workflows-cwl.yaml
Delete the pod

You will need to delete the pod if you want to re-create it.

Delete created pod​

oc delete -f d2s-core/support/run-workflows-cwl.yaml