Enhancement kb

[kbpi314]

Pull Request Template for MMEDS

What has changed

picrust2.Snakemake is a new example rule file
picrust2.smk for pc2 analyses
file_manipulation.smk now handles fasta, tsv, and biom input

Checklist of pre-requisites

• Does the code run?
• Does the code follow the repository style?
• Is the code tested?

How to use the feature

-See picrust2.Snakemake for example

How the design has changed

-PICRUST2 is now a rule in functional_annotation.smk
-Expanded extract_feature_table.sh to process tsv, biom, and fasta files

Additional notes

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 65.43%. Comparing base (1b02243) to head (6349f7d).
⚠️ Report is 31 commits behind head on Enhancement-ImprovedSnakemakeFunctionality.

Additional details and impacted files

@@                             Coverage Diff                             @@
##           Enhancement-ImprovedSnakemakeFunctionality     #475   +/-   ##
===========================================================================
  Coverage                                       65.43%   65.43%           
===========================================================================
  Files                                              25       25           
  Lines                                            4554     4554           
===========================================================================
  Hits                                             2980     2980           
  Misses                                           1574     1574           

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[adamcantor22]

i will make these small changes myself, thanks for writing this

[adamcantor22]

@kbpi314 for future reference, branch should be named more verbosely :p