Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

Easy fix in the documentation in hte Running section

YatrosYatros Seattle, WA, USAMember ✭✭


I was following your documentation to get familiarized with WDL. When I was trying to run WDL on Cromwell locally I was getting the error

Error: Unknown argument 'myWorkflow_inputs.json'

If you read the software's help you can easily figure out that there is a '-i' missing in the documentation command, but it will be better for inexperienced people to get it fixed.

Running WDL on Cromwell locally

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:

Instead of:

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

the command should look like this:

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

Thanks for the detailed documentation you are putting together to understand how to use WDL with Cromwell.




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