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Cromwell hangs at "Starting" execution status when using select_first on an optional Array

markwmarkw Cambridge, MAMember, Broadie, Dev ✭✭
edited February 2019 in Ask the Cromwell + WDL Team

Cromwell (v36 server mode w/ Google Cloud backend) has been hanging for a particular task. In the metadata, the task is stuck showing executionStatus: "Starting", but never starts (even after 20 hours). I have narrowed down that this happens due to a select_first() statement like this:

version 1.0
task MyTask {
  input {
    Array[String]? optional_string_array
  }
  Array[String] string_array = select_first([optional_string_array, []])
}

As far as I can tell, this is perfectly valid WDL code. Either way, there was no way to track down the cause without removing code one line at a time. In my case, I was passing in an Array[String] with a single element. I didn't test whether this occurs when the input is omitted.

This workaround doesn't seem to cause any problems:

Array[String] disabled_read_filters_list = if defined(disabled_read_filters) then disabled_read_filters else []
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