+ 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
You can get rid of a temp var and more properly scope $i with something like this:
```
for (my $i = 0; $i < @paths; $i++) {
    if ($paths->[$i]->is_dir) {
        $self->debug_message('---> [%d] (Directory) %s', $i, $paths->[$i]);
    } else {
        $self->debug_message('---> [%d] (File) %s', $i, $paths->[$i]
    }
}
```

You can even combine the if/else branches by using a conditional
```
my $tag = $paths->[$i]->is_dir ? 'Directory' : 'File';
$self->debug_message('---> [%d] (%s) %s', $i, $tag, $paths->[$i]);
```