Enhancement snakemake analysis

[adamcantor22]

Pull Request Template for MMEDS

What has changed

This PR will move MMEDS analysis from a structure using "Tool" classes -- individual files for each process with decentralized ability to be modified -- to a central Analysis class that makes use of snakemake workflows. The two workflows included in this release are a 'core_pipeline_taxonomic', replacing and improving on the old "Qiime2" tool, and 'lefse', a vast improvement over the old lefse tool.

Checklist of pre-requisites

• [x] Does the code run?
• [x] Does the code follow the repository style?
• [x] Is the code tested?

How to use the feature

Analyses are started in the same ways they were previously: running the script run_analysis.py, or navigating to the Analysis page of the website and putting the information in there. There are new config templates, those can be found in resources under config_file.yaml and lefse_config.yaml.

Additional notes

I've decided to deprecate summaries for now. They're odd at best and usually completely useless in their current form. Leaving the summary file in entirely commented to allow for future reference or support.

Issue Closings

Closes #466 Closes #457 (will move the relevant comments to a new issue) Closes #449 Closes #386 Closes #400 Closes #430 Closes #438 Closes #437 Closes #382

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 82.23496% with 62 lines in your changes missing coverage. Please review.

Project coverage is 64.16%. Comparing base (8cc4397) to head (5125c48).

Files with missing lines	Patch %	Lines
mmeds/tools/analysis.py	85.87%	38 Missing :warning:
mmeds/spawn.py	15.38%	11 Missing :warning:
mmeds/server.py	0.00%	6 Missing :warning:
mmeds/util.py	84.61%	4 Missing :warning:
mmeds/config.py	90.47%	2 Missing :warning:
mmeds/database/documents.py	83.33%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #472 +/- ## ========================================== + Coverage 60.12% 64.16% +4.04% ========================================== Files 32 25 -7 Lines 5783 4507 -1276 ========================================== - Hits 3477 2892 -585 + Misses 2306 1615 -691 ```

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