Place a dough hook on a stand mixer. Combine the flour with the nutmeg, yeast, salt, EVOO and pepperoni. Mix for a couple of minutes on medium, then crank the the mixer speed up to high and let the dough work for 10 minutes. Transfer the dough to a floured surface and let rest for 10 minutes.
Cut the dough into six parts and roll them into small balls. Cover and let rest for 10 more minutes. Roll each dough into an 18-inch rope and twist into a pretzel. Let the pretzels poof for 45 minutes in a warm area, uncovered.
Let the pretzels rest in the refrigerator uncovered for at least 2 hours, or overnight.
Pre-heat the oven to 400°F.
Mix the baking soda and 2 quarts boiling water together and boil the pretzels for 30 seconds each.
Remove and place the pretzels onto a greased nonstick baking sheet. Sprinkle each pretzel with coarse salt, sesame seeds, onion flakes and garlic and bake for 10 minutes.
Serve with mustard dipper.