Consider adding option to run abricate on assemblies

[dfornika]

We have a use-case where we'd like to routinely run abricate to detect resistance genes on bacterial assemblies generated with this pipeline. We have a couple of options on how to handle this:

• Add an optional abricate process to this pipeline
• Create a new pipeline that's focused on running abricate

I think it's generally preferable to keep the scope of a pipeline as focused as possible, to avoid "scope creep" that can lead to accumulating complexity within the pipeline. But this may be a good opportunity to provide support for resistance gene detection in a single place that could be available to multiple projects or use-cases.

There is some precedent to taking the alternative approach of creating a separate pipeline, which is what we did for our BCCDC-PHL/mlst-nf pipeline.