Optional case counts, PE, and SR file inputs for SingleSample workflow

[mwalker174]

Lets users bypass Module00a in the SingleSample workflow.

[cwhelan]

This looks good to me, nice addition.

I have one tiny complaint about the preexisting but related code: one thing that always trips me up when I follow the logic around whether 00a gets run is that running the callers in 00a is triggered by the docker string inputs being defined, and that we purposefully set them to undefined by setting them to NONE_STRING_, which should never be defined. It makes me want to rename NONE_STRING_ to UNDEFINED_STRING_ to help me remember what it is. I know we follow a similar pattern in other WDL files, though, so if other people don't have the same problem remembering it that I do then feel free to ignore this.

[mwalker174]

Thanks @cwhelan. I chose NONE_STRING_ because None is the null type identifier for WDL (see openwdl/wdl#263). I'm not opposed to UNDEFINED_STRING_ either, though it would be better if we could find a way to avoid using this hack in the first place.