Merge develop/ref culling into develop/nextflow

Nextflow scripts added:

• ref_culling.nf

Scripts added:

• collect_kmers.sh
• align_reads.sh
• cull_reference_candidates.py
• Cull_Reference_Candidate.cpp:
  • Cmdopt.cpp
  • cmdopt.hpp
  • process_map.cpp
  • process_map.hpp