This is the fungal disease 'Black Knot'.  This is a common disease of chokecherry, particularly its many cultivars, and the Mayday tree (a European cherry).  There is no cure for the disease.  You can prune out every knot and they will come back as the first year infections are very difficult to detect, only a slight swelling on the shoot, and these need to be pruned out as well.  There is a wide variation in resistance and trees that have the disease will always have the disease so removal is the best option.