Refactor needed to remove duplicated lines after PacBio addition.

[antgonza]

Original PR: https://github.com/qiita-spots/qp-knight-lab-processing/pull/143/files.

The main methods that need some refactor are:

1. split_similar_size_bins -> if/else allow_fwd_only blocks
2. demux_just_fwd_processing -> demux_cmd
3. nuqc_job.sh & nuqc_job_single.sh

Now, while doing this it might be nice to reconsider what needs to live in this repo and kl-metapool; my guess is that we can move a lot of the prep creation here.

[AmandaBirmingham]

Amen to the note about reconsidering what belongs in this repo and in kl-metapool. Cross-linking to the issue I put there: biocore/kl-metapool#335