Migrate "Tools" framework to snakemake workflows

[cleme]

Is your feature request related to a problem? Please describe.
Including additional tools in MMEDS should be simply a matter of defining inputs, outputs, and command calls. It is unclear whether the current implementation of MMEDS is similar to this or requires ad hoc code.

Describe the solution you'd like
Review current implementation. Discuss whether it is sufficiently robust or we need an alternative approach.

[adamcantor22]

We have discussed this a lot, but never written it down: all analyses should ideally be contained within snakemake files (Nextflow would be the other viable workflow system, but snakemake works out of the box with python) for easy structuring and modification. This will likely have to be the centerpiece of its own release

[adamcantor22]

For my first pull request of this release, I'll only be adding two workflows: 'standard_pipeline' and 'lefse'. This is just to establish the framework, as well as most of the generic use cases that will be used by most other workflows. Attaching here the issues for tools that will become workflows (by themselves or in conjunction with other tools) in the following pull requests:
-SparCC & Cytoscape: #307
-DMM: #378
-Batch Correction: #381 (should batch correction be automatic in the standard pipeline? should it be separate?)
-Decontam: #412
-rPCA: #443
-UMAP: #444
-RF/Lasso: #468

Others that will need to be added or re-added:
-CUTIE
-PiCRUSt2 (and BRITE)
-Mediation
-Everything shotgun related