howto Run a WDL script via Cromwell on a local machine eg your laptop

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created by Geraldine_VdAuwera

on 2015-12-21

Running on a local machine is the simplest thing in the world. Assuming that you have a WDL script that you’ve [validated](https://software.broadinstitute.org/wdl/userguide/validation.php) called `myWorkflow.wdl`, and a [JSON file of inputs](https://software.broadinstitute.org/wdl/userguide/inputs.php) 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:

Updated on 2017-09-30