Optional parameters with defaults can not be overridden by inputs.json

Say I have a task called bwaMem in a workflow called alignment.

The task bwaMem looks as follows.

task bwaMem {
  File in1
  File? in2
  String indexBase
  Int? threads = 1
  command {
   bwa mem ${"-t" +threads}  ${indexBase} ${in1} ${in2}
  }
  output {
    File samFile = glob(*.sam)
  }
 runtime {
  cpu = select_first([threads])  
  }
}

Then I can use the following inputs.json for the workflow alignment:

{
  "alignment.bwaMem.threads": 3
}

But this is ignored. The default value of 1 is used. On the contrary, if I set defaults for the alignment workflow itself. I can override these in the inputs.json. But apparently this does not work for imported tasks?

[cjllanwarne]

I agree that optional task inputs not being overridable from the inputs json is a bug and should be fixed.

Regarding defaults vs fixing values, you’re both right - values like that might be intended as inputs or might be intended as fixed intermediate values depending on the context and it’s really hard to deduce which one an author intended just based on the WDL file.

That kind of confusion is exactly why WDL 1.0 (you’re currently writing in draft-2) is adding input sections. Ie:

workflow foo {
  input {
    # input with default
    Int threads = 1
  }
}

vs

workflow foo {
  input {
    ...
  }
  
  # intermediate value: cannot be overridden
  Int threads = 1
}

[rhpvorderman]

Closed as not an issue anymore in 1.0