Merge pull request #112 from teharrison/master

fix fix stage
No longer using a separate pipeline configuration.
Merge pull request #113 from jaredbischof/master

No longer using a separate pipeline configuration for this script.
Fixed script name in usage message.
Merge pull request #114 from jaredbischof/master

Fixed script name in usage message.
Changed default allocation of cpus and memory.
Added sort memory as an option and passed that to sims2annotation script.
Merge pull request #115 from jaredbischof/master

Added sort memory as an option and passed that to sims2annotation script.
Fixed printed script options.
Merge pull request #116 from jaredbischof/master

Fixed printed script options.
Fixed filename.
Merge pull request #117 from jaredbischof/master

Fixed filename.
Removing files from list of required output files that are no longer going to be generated by pipeline.
Merge pull request #119 from jaredbischof/master

Removing files from list of required output files that are no longer going to be generated by pipeline.
Changing file output names.
Changing output filenames.
Changing input file names.
Merge pull request #120 from jaredbischof/master

Changing some pipeline file names.
Adding a couple filename variables that are being used temporarily by old pipeline.
Merge pull request #121 from jaredbischof/master

Adding a couple filename variables.