Unexpected conversion of Map[String, Array[String]] to Array[Pair[String, Array[String]]]

[williamrowell]

Example:

version 1.0

workflow wf {
  input {
    Map[String, Array[String]] input_stats = {
      "stat1": ["1", "2", "3"],
      "stat2": ["D", "E", "F"]
    }
  }
  call t {
    input:
      stats = input_stats
  }
  output {
    File out = t.out
  }
}

task t {
  input {
    Map[String, Array[String]] stats
  }
  command <<<
    cat "~{write_json(stats)}"
  >>>
  output {
    File out = stdout()
  }
}

Expected output:

{"stat1": ["1", "2", "3"], "stat2": ["D", "E", "F"]}

In miniwdl, write_json() converts Map[String, Array[String]] into an object, as expected and defined in the 1.0 spec.

Actual output:

[{"left":"stat1","right":["1","2","3"]},{"left":"stat2","right":["D","E","F"]}]

Cromwell (v90) seems to be storing or converting the Map[String, Array[String]] as Array[Pair[String, Array[String]]], and write_json() converts it into an array of objects.

Simpler structures like Map[String, String] seem to behave as expected in Cromwell.