Standarizing pipeline elements and removing artifacts of previous versions

[agthomas-ucsb]

We will work this spring quarter to find quirks in the pipeline that we can remove to make it easier for internal and external use. One such example is "-r" vs "-n" for the read argument passed from the command line. Many elements of the pipeline are outdated and no longer useful. These should be removed to expedite the pipeline's processing speed and hit real time goals.