Conditional statement

It is often desirable to only execute some section of a computation graph only if a particular condition holds. This could be as simple as a user input to the workflow indicating the "mode A" should be run instead of "mode B", whether to scatter and gather tasks rather than running a single multi-threaded task, or enabling an entire analysis based on if some analytical check passes a QC threshold. In these cases, you'll want to reach for conditional statements (also known as if/else statements).

This often takes a form similar to the following example.

# ... task definitions ...

workflow run {
  inputs {
    Boolean perform_further_work = true
  }

  # Run the first task.
  call stepA {}

  # If the conditional is true, run `stepB` and `stepC`.
  if (perform_further_work) {
    call stepB { input: in = stepA.out }
    call stepC { input: in = stepB.out }
  }
}

This can also take the form of evaluating outputs from prior workflow steps. For example, if you had a task stepA that contained a Boolean is_sufficient_quality output, you could do the following.

# ... task definitions ...

workflow run {
  # Run the first task.
  call stepA {}

  # If `stepA` determined the sample is of sufficient quality,
  # run `stepB` and `stepC`.
  if (stepA.is_sufficient_quality) {
    call stepB { input: in = stepA.out }
    call stepC { input: in = stepB.out }
  }
}