I have celiac disease and discovered this cafe by chance during my visit to Lyon. I ate the very tasty sandwiches there twice. The gluten-free rolls were really tasty and cost an extra €1. There is no guarantee of freedom from contamination because there is no separate gluten-free work area, but on both occasions the various servers were knowledgeable about celiac disease and did their best in the preparation (changing gloves, using clean utensils, etc.)
I didn't have any problems after any of the visits.