Preheat oven to 350 degrees F. Line baking sheet with parchment paper or a silicone baking mat.
Place pecans, coconut flakes, and oats in a skillet and toast over low heat until fragrant, stirring often, about 5 minutes. Set aside to cool.
Using an electric mixer on medium speed, cream together butter and sugar until light and fluffy. Add eggs and vanilla and mix until well combined.
In a medium bowl, whisk together whole wheat flour, wheat germ, baking soda, and salt. Add to the butter mixture and mix on low speed until just combined. Fold in the chocolate chips, pecans, coconut flakes, and oats.
Scoop dough by the tablespoonful (I use this cookie scoop) and place on the baking sheet, spacing about 2 inches apart. Bake cookies for 9-10 minutes, until lightly golden.