Miniwdl fails on list with optional outputs even though select_all is used

[rhpvorderman]

See #613 that contains a minimum reproducible example.

[mlin]

Thanks @rhpvorderman, quickly I was able to trace the root cause to a hacky workaround mentioned here, which has come back to bite me. I probably want to replace the hack with some proper solution, but need to think about what that will be.

miniwdl/WDL/runtime/task.py

Lines 665 to 667 in 0dc9a21

	# We may overwrite File.value with None, which is an invalid state, then we'll fix it
	# up (or abort) below. This trickery is because we don't, at this point, know whether
	# the -declared- output type is optional.

[rhpvorderman]

Yeah, this will result in a Array[File] with a None inside because the coercion to None is done after the select_all. At least that is how I understand the code.

It can be easily fixed by a hacky workaround elsewhere (if v.value is None return os.devnull) but that would make the codebase such a mess 😅 .

[mlin]

I have a fix in #615, I think it's the right approach but still needs a bit of polishing.

[rhpvorderman]

Nice! I currently have other priorities I need to attent to, but as soon as I have the time I will try out the branch on our WDL codebase.