Prevent pegasus-lite failure when user passes -w to docker

Pegasus Lite invokes the user script as follows

su $cont_user -c \"./6mAcalling_1_extractCCS_ID0000001-cont.sh \"

The above breaks if the user overrides docker command with -w flag.

Consider changing the invocation to

su $cont_user -c \"/scratch/6mAcalling_1_extractCCS_ID0000001-cont.sh \"

and the cont.sh file should execute cd `dirname $0`