Preheat the oven to 200C/400F/Gas 6. Oil a 12-hole muffin tin and line with 12 squares of baking paper. Push the squares down into each hole so that the paper sticks up.
Sift the flours, baking powder, and bicarbonate of soda into a large bowl. Stir in the salt and rosemary. (Reserve any wholegrain left in the sieve.)
Meanwhile in another bowl, mix the eggs, yoghurt, milk, honey and vegetable oil until well combined.
Pour the wet ingredients into the dry and fold the ingredients together, but be careful not to over-work the mixture. Stir in most of the pumpkin, reserving a little for the top of the muffins. Spoon the mixture into the muffin cases.
Sprinkle the reserved wholegrain, pumpkin and the pumpkin seeds over the muffins. Bake in the centre of the oven for 20–25 minutes, or until the muffins are well risen and a skewer inserted in the centre comes out clean.