Cobalt as of version 0.99.28 supports placing qsub arguments.
Cobalt sets a variety of environment variables for the user's conveinence
If the block is a BlueGene/Q subblock then the following are set:
#COBALT -n 512
#COBALT -t 1:00:00
#COBALT -A MyProject
#COBALT -q prod
runjob --block $COBALT_PARTNAME : myExecutable