If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
(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: