I'd have to check but I think the 12th sailed out of Bordeaux.
Edit: Taken directly from the GWX manual:
BdU founded the 12th Flotilla in Bordeaux, France on October 15, 1942 under the command of Korvettenkapitän Klaus Scholz, where it received its first U-boat on January 9, 1943. BdU assigned most of the long-range U-boats to this flotilla, which operated primarily in the South Atlantic and Indian Oceans. The 12th Flotilla disbanded and sent its surviving U-boats to Flensburg in August 1944; the Allies captured Scholz and his remaining shore-based personnel as they were trying to return to Germany through France
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