Cleanup command line builder

[illusional]

I've never really been happy with the command line builder - this has sort of led me to half-implement building the command line with wdlgen, and half in an external project.

I guess it depends what you want from this project, but I don't believe the core should be taking care of that for you - I believe it should be a more faithful representation of WDL.

For this reason, in v0.3.0 I've removed the option to provide components to the Task.Command.CommandInput (which would construct the workflow for you). This behaviour will still exist temporarily in in Task.Command.CommandInput.from_fields, but with a number of PRs coming to cleanup these string interpolation options and provide a quoting mechanic, I don't think we need to do this.

[illusional]

Hey @TMiguelT, just FYI for this PR and v0.3.0 release.

Specifically removing the interpolation options for these reasons:

• Clarify the expression placeholder and string interpolation behaviour #229
• Added Suffix and similar Quoting Engine Functions

I'll attach the code I now use for quoting the command line. I use the updated sep function (because I implemented in Cromwell and miniWDL), and once the quoting functions are implemented I'll merge those in. For transparency, I'm not attempting to generate especially readable code, purely functional :

https://github.com/PMCC-BioinformaticsCore/janis-core/blob/cb1e87a3440a8920afe8d21f840b1f6bfaf39ba7/janis_core/translations/wdl.py#L976-L1066

Edit: Fixed a few things with my binding (optional arrays, arrays of optional types, prefix generation for arrays)

[illusional]

The OpenWDL PR has been merged, including implementations in Cromwell and MiniWDL - so this will merge.
I've added a change to remove the command options so they should work forwards. If you need the current existing functionality, you'll need to illusional.wdlgen to <0.3.0, eg:

https://github.com/PMCC-BioinformaticsCore/janis-core/blob/93f6e1aaba4d4c221706f2ad0aa73b6d884ebb46/setup.py#L55