Update AmpIllumina GL-DPPD-7104-C pipeline doc (#175)

* Updated Amplicon Seq pipeline doc
  - add zipped files and zip steps
  - rarefaction_depth.txt files
  - assay_suffix added throughout
  - sync alpha/beta diversity code
  - failure file notes
  - add tech_type filename placeholder

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Co-authored-by: Jihan Yehia <[email protected]>

Author: bnovak32