Validate workflow scripts#

The WOMtool program provides a utility to perform a full validation of your WDL scripts, including syntax and semantic checking.


This tutorial will help you validate your WDL scripts.


Before you begin, you will need the following:

Run the WOMtool#

Use the following command to validate your WDL script:

java -jar womtool.jar validate MyMainWorkflow.wdl

Once validated, you can also run and test your WDL workflow locally by providing the updated input JSON file along with your workflow scripts to the Cromwell run command (external link).

java -jar cromwell.jar run --inputs MyMainWorkflowInputs.json MyMainWorkflow.wdl

The SeqsLab platform provides the fully-managed WDL workflow execution environment agnostic to the underlying computing and storage infrastructure. When you are ready to run your workflow production on the SeqsLab platform, you simply provide the inputs JSON file along with the WDL workflow scripts and SeqsLab Jobs will streamline the process of connecting input/output datasets, parallelizing workload processing, and provisioning optimal computing resources.