This documentation is in the process of being updated. In the meantime, you may find that some GATK commands are out of date, or that the WDL information is incomplete. If you encounter any issues you can't solve, please let us know.

This section lays out all you need to know to start writing and running WDL workflows that do useful things -- TODAY.

Don't worry, this is going to be easier than you might think.

Writing a WDL

First, we'll introduce the building blocks of WDL and how they fit together to form the base structure of a WDL script. Then we'll show how to add variables so that input files and parameters can be specified outside of the script itself, which will allow you to use the same script for different runs without modification. Next, we'll cover how to add plumbing, i.e. how you can chain together the components that perform units of work in different ways to form sophisticated pipelines. Finally we'll look at how to validate syntax, which sounds boring but is really helpful since it will tell you quickly whether your WDL script is runnable or not. Because nobody likes starting a run only to see it fail because it's missing a semi-colon somewhere.

Running a WDL

This is going to be short and sweet. We'll show you how to generate a JSON template for specifying inputs (spoiler: it's super easy) and fill it out. Then we'll present the main options for executing your WDL script, focusing on the execution engine we use in our own work, which is called Cromwell. If you had asked us two years ago if we'd ever have an execution engine that we could use both in development and in production, locally and on the cloud, we would have said when pigs fly...

When you're ready

Once you have grokked the core concepts involved in writing and running WDL workflows, the next step will be to actually do it yourself! In the Tutorials section, we provide a series of fully worked-out "build-a-WDL" examples in which we walk you through each step of composing workflows that demo all the key features of WDL. For best effects, work your way through the tutorials in the order suggested on the Tutorials page.

To set up your computer to write and execute workflows, check out this tutorial.