Task Definition

A WDL task can be thought of as a template for running a set of commands - specifically, a Bash script - in a manner that is (ideally) independent of the execution engine and the runtime environment.

A task is defined using the task keyword, followed by a task name that is unique within its WDL document.

Tasks are comprised of the following elements:

• A single, optional input section, which defines the inputs for the task.
• A single, required command section, which defines the Bash script to be executed.
• A single, optional output section, which defines the outputs for the task.
• A single, optional requirements section, which defines the minimum, required runtime environment conditions.
• A single, optional hints section, which provides hints to the execution engine.
• Deprecated A single, optional runtime section, which defines the runtime environment conditions. This is mutually exclusive with the requirements and hints sections.
• A single, optional meta section, which defines task-level metadata.
• A single, optional parameter_meta section, which defines parameter-level metadata.
• Any number of private declarations.

There is no enforced order for task elements.

The execution engine is responsible for "instantiating" the shell script (i.e., replacing all references with actual values) in an environment that meets all specified runtime requirements, localizing any input files into that environment, executing the script, and generating any requested outputs.

task name {
  input {
    # task inputs are declared here
  }

  # other "private" declarations can be made here

  command <<<
    # the command template - this section is required
  >>>

  output {
    # task outputs are declared here
  }

  requirements {
    # runtime requirements are specified here
  }

  hints {
    # runtime hints are specified here
  }

  meta {
    # task-level metadata can go here
  }

  parameter_meta {
    # metadata about each input/output parameter can go here
  }
}