(howto) Run a WDL script via Cromwell on a local machine (e.g. your laptop)

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
edited September 2017 in Tutorials

Running on a local machine is the simplest thing in the world. Assuming that you have a WDL script that you've validated called myWorkflow.wdl, and a JSON file of inputs called myWorkflow_inputs.json, you just call Cromwell’s run function, like so:

java -jar Cromwell.jar run myWorkflow.wdl --inputs myWorkflow_inputs.json

This will run your workflow. You will see text from the Cromwell engine updating you as it walks through the steps.

Note that any messages that are normally output to the terminal by the tools themselves will not actually be shown in the terminal where you're running the script. Instead, Cromwell saves this output in a log file called stderr located within the execution folder.

By default, you can find all generated files (outputs and logs) in this folder:


Post edited by Geraldine_VdAuwera on
Sign In or Register to comment.