remove directory param from torque qsub (#3080)
remove directory param from torque qsub (#3080)

Cromwell creates directory trees with long names, which causes torque to throw
```
qsub: -d arg is longer than 256 characters
usage: qsub [-a date_time] [-A account_string] [-b secs]
      [-c [ none | { enabled | periodic | shutdown |
      depth=<int> | dir=<path> | interval=<minutes>}... ]
      [-C directive_prefix] [-d path] [-D path]
      [-e path] [-h] [-I] [-j oe] [-k {oe}] [-l resource_list] [-m n|{abe}]
      [-M user_list] [-N jobname] [-o path] [-p priority] [-P proxy_user] [-q queue] 
      [-r y|n] [-S path] [-t number_to_submit] [-T type]  [-u user_list] [-w] path
      [-W otherattributes=value...] [-v variable_list] [-V ] [-x] [-X] [-z] [script]
```

`cd`-ing to the directory beforehand fixes this.

Cheers
M
a113n/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lbeltrame/bcbio-nextgen,chapmanb/bcbio-nextgen,chapmanb/bcbio-nextgen,a113n/bcbio-nextgen,vladsaveliev/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lbeltrame/bcbio-nextgen,lbeltrame/bcbio-nextgen,a113n/bcbio-nextgen,chapmanb/bcbio-nextgen