Typo fix, more shell updates
Typo fix, more shell updates

Fixed a problem with calling macs2. Better file naming. Deleting more
files that aren't needed after running as shell.

frazer-lab/pipelines,cdeboever3/cdpipelines,frazer-lab/pipelines,cdeboever3/cdpipelines,cdeboever3/cdpipelines,frazer-lab/pipelines