Edited pipeline_annotation stage to only pass to sims2annotation bin script, only the files (from aa sims file, rna sims file, aa mapping file, and rna clustering file) that are nonzero size.  This should make it possible for a job to continue running even if some of these files are zero size.
Merge pull request #151 from jaredbischof/master

Edited pipeline_annotation stage so it should allow for empty aa sims or rna sims file, but not both.