This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
(howto) Run a WDL script via Cromwell on a local machine (e.g. your laptop)
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: