Rename `Snakefile-full` to `Snakefile-zymo` and decouple the rules

[SamStudio8]

The Zymo benchmark is pretty useful to us. The Snakefile-full rule set is a holdover of the work I did for our mock community GigaScience paper. It's likely given all the recent developments to Snakefile-base that the rules won't work together properly anymore. It would be good to bring this back from the dead and take the opportunity to have a fully contained reticulatus self-test in the form of a Zymo pipeline. I'll use this issue as a tracking issue.

• [x] Rename the rule set
• [x] checkm install and merging
• [x] Automatically download the McIntyre references instead of requiring them
• [ ] Automatically download the static kraken files included in the paper
• [x] Incorporate @nickloman's alignment stats step
• [x] Incorporate the assembly quality script as a new rule

[SamStudio8]

it begins

[SamStudio8]

Added fastmer!

[SamStudio8]

The mechanism for downloading references has already been implemented in the new ref.cfg stuff

[SamStudio8]

Automatically download the static kraken files included in the paper

I don't think this is actually in the scope of reticulatus. Instead, we'll want a way to mock entries into manifest.cfg so the generation of reports is taken care of the right way.

[SamStudio8]

Opened #37 to track the last feature request. Otherwise the Snakemake-zymo steps emulate the old mock community pipeline (and more!).