Do not specify workDir

The working directory that is set with --workDir mostly contains book-keeping files. These files need to be on a POSIX-compliant file system, because it must be possible to lock them to guarantee exclusive access. If the working directory is on an NFS mounted file system, all kinds of race conditions may occur, because file locking doesn't work reliably on NFS. By default, the working directory will be created in the local temporary directory, pointed to by, e.g. $TMPDIR, or $TEMP.

I've removed the command-line option --workDir from the scripts that use Toil as workflow engine.