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 whether 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.

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# ... task definitions ...

workflow run {
  input {
    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 { value = stepA.out }
    call stepC { value = 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.

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# ... 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 { value = stepA.out }
    call stepC { value = stepB.out }
  }
}

Using else and else if

When you need to execute one branch or another based on a condition, use else. For multiple conditions, chain else if clauses together.

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# ... task definitions ...

workflow run {
  input {
    String mode
  }

  if (mode == "fast") {
    call fast_analysis {}
  } else if (mode == "thorough") {
    call thorough_analysis {}
  } else {
    call standard_analysis {}
  }
}