Task

The task component is a top-level component of WDL scripts. It contains all the information necessary to "do something" by using a command along with definitions of input files and parameters, as well as the explicit identification of its output(s) in the output component. It can also be given additional (optional) properties using the runtime, meta and parameter_meta components.

Tasks are "called" from within theworkflow, which is what causes them to be executed when we run the script. The same task can be run multiple times with different parameters in the same workflow, which makes it very easy to reuse code. See Task aliasing for more information.

Example:

task task_A {
  input {
    File ref
    File in
    String id
  }
  command <<<
    do_stuff -R ~{ref} -I ~{in} -O ~{id}.ext
  >>>
  runtime {
    docker: "ubuntu:latest"
  }
  output {
    File out = "~{id}.ext"
  }
}