An Example Workflow

Below is the code for the "Hello World" workflow in WDL. This is just meant to give a flavor of WDL syntax and capabilities - all WDL elements are described in detail in the Language Specification.

Example: hello.wdl

version 1.3

task hello_task {
  input {
    File infile
    String pattern
  }

  command <<<
    grep -E '~{pattern}' '~{infile}'
  >>>

  requirements {
    container: "ubuntu:latest"
  }

  output {
    Array[String] matches = read_lines(stdout())
  }
}

workflow hello {
  input {
    File infile
    String pattern
  }

  call hello_task {
    infile, pattern
  }

  output {
    Array[String] matches = hello_task.matches
  }
}

{
  "hello.infile": "data/greetings.txt",
  "hello.pattern": "hello.*"
}

{
  "hello.matches": ["hello world", "hello nurse"]
}

This WDL document describes a task, called hello_task, and a workflow, called hello.

• A task encapsulates a Bash script and a UNIX environment and presents them as a reusable function.
• A workflow encapsulates a (directed, acyclic) graph of task calls that transforms input data to the desired outputs.

Both workflows and tasks can accept input parameters and produce outputs. For example, workflow hello has two input parameters, File infile and String pattern, and one output parameter, Array[String] matches. This simple workflow calls task hello_task, passing through the workflow inputs to the task inputs, and using the results of call hello_task as the workflow output.