Override an optional with null

[orodeh]

This is related (at least) to #2446.

Examine the workflow wf below.

workflow wf {
    String? who

    call hello { input:
        who = who
    }
}

task hello {
    String? who = "world"

    command {
        echo "Hello, ${who}"
    }
    output {
         String result = read_string(stdout())
    }
}

When running wf with Cromwell v32 the result is hello.result = "Hello, world". However, since we are calling the task with an empty value, it should override who, and the the result should be (I think) Hello,".

[aednichols]

Thanks for reporting.

I think Cromwell is having trouble because it can't distinguish between

wf specifically set who to null, so don't accept the default in hello

and

wf does not set who, so accept the default in hello

because it's just null either way!

[aednichols]

With inputs

{
  "wf.input_to_wf": null
}

and WDL

version 1.0

workflow wf {
    input {
        String? input_to_wf = "Neither should this"
    }

    call hello { input:
        input_to_hello = input_to_wf
    }
}

task hello {
    input {
        String? input_to_hello = "This should not be here"
    }

    command {
        echo "Should be blank: ${input_to_hello}"
    }
    output {
         String result = read_string(stdout())
    }
}

the result is

"Should be blank: This should not be here"

...so it would seem that Cromwell understands not to overwrite null with a default value sometimes, just not on calls.