Leo Moreno

Trying the example above worked, but it seems to be that cromwell fails to capture docker ran jobs? Here is a more detailed example: ``` version development workflow wf {...

> I think maybe your tool outputs lines to the console, but they aren't actually going to the `stderr` and `stdout` streams. Yes I have tried Paul's example and it...

I think I found the issue. In my script.submit I am getting: ``` mkfifo: cannot create fifo '/cromwell-executions/wf/87c7dfae-7ad1-4435-960b-a2ecff96c90d/call-trinity/tmp.bb40533c/out.1': Operation not permitted mkfifo: cannot create fifo '/cromwell-executions/wf/87c7dfae-7ad1-4435-960b-a2ecff96c90d/call-trinity/tmp.bb40533c/err.1': Operation not permitted /cromwell-executions/wf/87c7dfae-7ad1-4435-960b-a2ecff96c90d/call-trinity/execution/script:...

If you are a Mac user and are also experiencing this issue, you have to compile cromwell from source and change file `backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala` as so: ``` - |mkfifo "$$$out" "$$$err"...