Added clustering.py, config.py, helper.py, reference_pipeline.py, trimmer.py

clustering.py
Uses MOTHUR to cluster sequences based on a DNADIST distance matrix

config.py
Module containing paths to executatbles and scripts to be called by Ruffus pipelines

helper.py
Some helper scripts

reference_pipeline.py
Ruffus pipeline for preprocessing refernce files from clustering to BWA index generation

trimmer.py
Ruffus pipeline for trimming sequences by similarity to a reference using BLASTn