Adding a QUAST module

[KevinMenden]

This PR adds a QUAST module.

To accommodate the two usecases of running quast with and without a reference genome, I ended up creating two modules, or "tools" for QUAST. I tried out a few things but as of now there's really no good way of dealing with optional inputs in DSL2. Until that's possibly, I think this is an adequate solution.

Let me know if you find any bugs or anything I should change :)

[drpatelh]

Thanks @KevinMenden . Ok, I think I have a solution that allows us to keep this repo clean from duplicating modules to deal with optional inputs. It's not ideal but possibly the best solution that allows developers to use their own parameter names e.g. instead of params.gff, params.fasta etc.

    input:
    path consensus
    path fasta
    path gff
    val use_fasta
    val use_gff

If we add two more boolean variables to the input then these can be evaluated in the script section to stage the appropriate file. This means we don't have to use params.gff anymore and keeps the module as clean as possible in terms of parameter names. Also, we get to keep a single instance of the module which I think is best given that this issue is really Nextflow specific. If/when optional inputs are supported we update the module. Simples.

What do you think?

[KevinMenden]

Okay yes, it's the best we can do right now I reckon :/
I agree this is nicer than having two different 'modules' for quast.

The only thing I'm a bit worried is how the fasta and gtf paths are evaluated, we probably need to pass some dummy values to them that look look like paths (basically just ""). I will test around a bit.

Thanks @drpatelh ! Will ping you when I've changed it.

[drpatelh]

Cool. Yup, that is exactly what I do if params.gff hasn't been provided. See here. This ensures that a file is always staged regardless of whether it needs to be used.

[KevinMenden]

@drpatelh okay everything refactored now :)

[drpatelh]

Amazing! Thanks @KevinMenden . Few minor changes. I find it more intuitive grouping by variable type than by name.

[KevinMenden]

Alright thanks for the review!