run.py needs to be updated

[dacb]

Issues noticed by @dacb and @erinhwilson:

• During indexing of the bam file, the .sorted.bam is appended twice to the file name
• When run in output as scripts mode, the faidx and file removal commands are not saved in the script
• When run in output as scripts mode, the faidx command should not be run

[dacb]

Additional opportunities:

• The parallelization engine does the jobs for each step in parallel then moves to the next step. This assures the operations on any file are atomic, but it causes a condition where the paralyzation engine is not fully loaded.