Preheat oven to 350°F. Line baking trays with parchment paper and set aside.
Whisk the flour, wheat germ, flaxseed, baking soda and salt in a bowl.
In a large bowl with a handheld electric mixer or in the bowl of a standing mixer fitted with the flat beater, mix together the coconut oil and butter.
Blend in the brown sugar and granulated sugar. Beat in the eggs and vanilla extract.
Gradually mix in the dry ingredients.
Stir in the chocolate chips.
Scoop some dough into a disposable decorating bag or freezer-safe Ziploc bag and close tightly with a rubber band. Snip 1-inch from the tip and pipe dollops of dough, 3/4-inch across, on the baking tray.
Bake each tray for 10 to 15 minutes until golden brown. Let cool.