JSON Output Format

The outputs from a workflow invocation may be serialized as a JSON object that contains one member for each top-level workflow output; subworkflow and task outputs are not provided. The name of the object member is the fully-qualified name of the output parameter, and the value is the serialized form of the WDL value.

Every WDL implementation must provide the ability to serialize workflow outputs in this standard format. It is suggested that WDL implementations make the standard format be the default output format.

For example, given this workflow:

workflow example {
  ...
  output {
    String foo = cafeteria.inn
    File analysis_results = analysis.results
    Int read_count = readcounter.result
    Float kessel_run_parsecs = trip_to_space.distance
    Boolean sample_swap_detected = array_concordance.concordant
    Array[File] sample_choices = choice_calling.vcfs
    Map[String, Int] droids = escape_pod.cargo
  }
}

The output JSON will look like:

{
  "example.foo": "bar",
  "example.analysis_results": "/path/to/my/analysis/results.txt",
  "example.read_count": 50157187,
  "example.kessel_run_parsecs": 11.98,
  "example.sample_swap_detected": false,
  "example.sample_choices": ["/data/patient1.vcf", "/data/patient2.vcf"],
  "example.droids": {"C": 3, "D": 2, "P": 0, "R": 2}
}

It is recommended (but not required) that JSON outputs be "pretty printed" to be more human-readable.

§File/Directory Outputs

It is up to the execution engine to provide workflow File and Directory outputs to the user that persist following a successful execution of the workflow. The execution engine is free to specify the values that are allowed for File and Directory parameters, but at a minimum it is required to support POSIX absolute file paths (e.g., /path/to/file).

It is strongly recommended that output files and directories be specified as absolute paths to local files or as URLs. If relative paths are allowed, then it is suggested that they be resolved relative to the directory that contains the output JSON file (if a file is written) or to a single common directory containing all the workflow outputs.