+ clean up FASTQs in /tmp after bwamem finishes aligning

- This is one of several immediate tasks that will help reclaim some
   of /tmp disk space that is being used with HiSeq X Ten data.  See
   [BIO-1229][1] for more details.

[1]: https://jira.gsc.wustl.edu/browse/BIO-1229
Why not just use -d $dir instead of the method call?