Developing a WDL Workflow

Toil can be used as a development tool for writing and locally testing WDL workflows. These workflows can then be run on Toil against a cloud or cluster backend, or used with other WDL implementations such as Terra, Cromwell, or MiniWDL.

The easiest way to get started with writing WDL workflows is by following a tutorial.

Using the UCSC Genomics Institute Tutorial

The UCSC Genomics Institute (home of the Toil project) has a tutorial on writing WDL workflows with Toil. You can follow this tutorial to be walked through writing your own WDL workflow with Toil. They also have tips on debugging WDL workflows with Toil.

These tutorials and tips are aimed at users looking to run WDL workflows with Toil in a Slurm environment, but they can also apply in other situations.

Using the Official WDL tutorials

You can also learn to write WDL workflows for Toil by following the official WDL tutorials.

When you reach the point of executing your workflow, instead of running with Cromwell:

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

you can instead run with toil-wdl-runner:

toil-wdl-runner myWorkflow.wdl --input myWorkflow_inputs.json

Using the Learn WDL Video Tutorials

For people who prefer video tutorials, Lynn Langit has a Learn WDL video course that will teach you how to write and run WDL workflows. The course is taught using Cromwell, but Toil should also be compatible with the course’s workflows.

WDL Specifications

WDL language specifications can be found here:

Toil is not yet fully conformant with the WDL specification, but it inherits most of the functionality of MiniWDL.