Amplicon Illumina nextflow conversion: Added Python wrapper script

[olabiyi]

I made the following changes:

1. Added a python wrapper script called run_workflow.py to run the workflow and set parameters.
2. Added sanity checks for input parameters and primers.
3. Modified the README file to include how to run the python wrapper script.
4. Modified the help message in main.nf with necessary parameter default changes.
5. Updated the pipeline document to include software updates and new differential abundance steps.
6. Fixed api error rate bug when running taxize to retrieve NCBI ids.
7. Fixed post processing bug to accurately retrieve raw read counts per sample.
8. Fixed software versions redundancy bug.
9. Added remove rare features / taxa and samples functionality with rare samples and taxa not filtered out by default.