WDL Documentation

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Documentation for the Workflow Description Language. For a gentle introduction on how to write WDL workflows, check out Getting Started with WDL.

• Frequently Asked Questions
• WDL Tutorials
• Plumbing Options
• Script Components
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• Getting Started with WDL

  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 an...
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• Base Structure

  There are 5 basic components that form the core structure of a WDL script: workflow, task, call, command, and output. There is no explicitly named "input" definition component; input variables (for specifying parameters as well as input and output...
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• Add Variables

  In this context, variables are placeholders that we write into the script instead of actual filenames and parameter values. We can then specify the filenames and values we want to use at runtime (meaning when we run the script) without modifying t...
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• Add Plumbing

  By plumbing, we mean chaining tasks together to form sophisticated pipelines. How do we do that in WDL? With effortless grace, that's how. Simple connections At this point you know how to include multiple tasks in your workflow script. If you we...
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• Validate Syntax

  Nobody likes to kick off a bunch of jobs only to find after returning from lunch that they all failed within minutes due to a syntax error in the script. Missing bracket, schmacket. The good news is that WDL comes with a utility toolkit called wdl...
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• Specify Inputs

    The simplest way to specify values for the input variables (such as file names and parameters) to the commands in your WDL scripts is to hard-code them, i.e. write them in the script itself. However, doing so forces you to make a new copy and ed...
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• Execute!

  At the moment, Cromwell is the only fully-featured execution engine that we know of that supports WDL. Cromwell Cromwell is an open source (BSD 3-clause) execution engine written in Java that supports running WDL on three types of platform: local...
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• Toolkit: All the tools you need to write and run WDLs

   AUTHORING SublimeText Our preferred editor for writing WDLs; it offers a good balance of usability and editing features. Syntax highlighters Plugins that enable syntax highlighting (i.e. coloring code elements based on their function) for suppo...
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