GATK wrappers should use workaround for optional arrays

[kshakir]

Until #25 is fixed, the gatk wrappers should not be using optional arrays, such as the intervals files. Instead they should use this bash workaround, with something similar to:

Array[String]? foo

command {
  if [ -n '${sep=',' foo}' ]; then
    FLAG=--prefix=${sep=',' foo}
  else
    FLAG=''
  fi

  echo $FLAG
}

[vdauwera]

So we never got around to fixing the GATK wrappers... do we still need to or is this handled in Cromwell 24?