Boundary conditions will allow you to simulate roughness along the walls of your pipe. For a no-slip boundary condition, usually one would be concerned with setting parameters such as roughness height, i.e. how far into the pipe from the wall's surface will roughness play a factor, and roughness constant - the degree of roughness of the pipe walls. The link I've provided below is a simple teaching lab which shows the study of flow in a pipe and goes in to the details of adding roughness into the walls.