Preheat oven to 350 degrees F. Line a 12 muffin tray with cupcake liners. In a large bowl, mix together whole wheat flour, rolled oats, baking soda, baking powder, ground cinnamon, nutmeg, cloves and salt. Mix them well and set aside.
In a separate bowl, start mixing the wet ingredients - whisk the eggs, brown sugar, then add pumpkin puree, melted butter, vanilla and yogurt. Mix all well until combined.
Mix the dry ingredients into the wet ingredients bowl. Add the chocolate chips and fold everything together gently until combined.
Scoop batter into prepared muffin tin, filling each cup but leaving some space for the muffins to fluff. Sprinkle with pumpkin seeds and rolled oats.
Bake for about 20 minutes or until toothpick inserted in the center of muffin comes out clean. Remove baking try from the oven. Allow muffins to cool before enjoying.