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Getting Started with WDL

Base structure
Add variables
Add plumbing
Validate syntax
Specify inputs
Execute!
Toolkit: All the tools you need to write and run WDLs

WDL Plumbing Options

Linear chaining
Branch and merge
Multi-input/Multi-output
Scatter-gather parallelism
Task aliasing
Conditional (if/else)

WDL Script Components

workflow
call
task
command
output
parameter_meta
meta
basename
Variable types in WDL

WDL Cookbook

Using task outputs downstream
Building multi-path workflows with branch and merge plumbing
Building multi-path workflows with conditionals and select_first()
Running a task with different parameters based on whether on optional input is defined
Running conditional tasks based on input size
Running conditional tasks based on optional inputs
Conditionally running different WDL tasks based on input data type
Parallelizing by scattering on an array
Scattering on an index
Scattering on optional types
Organize multiple inputs using structs

Community

Broad Pipeline Development Team
WDL at Fred Hutch

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