To make the Pipeade:
Heat 4 tablespoons oil in a large, lidded saute pan set over medium heat. Add the chorizo, and cook, stirring, until the sausage is evenly browned, about 4 minutes. Using a slotted spoon, transfer the chorizo to a plate.
Add the onion and red and green bell peppers to the pan; cook, stirring frequently and adjusting heat as necessary, so that nothing takes on color, until vegetables soften and onion turns translucent, 10 to 12 minutes.
Return chorizo to pan along with the tomatoes, garlic, and red pepper flakes; season with salt and pepper. Lower the heat, cover, and simmer 10 minutes more.
To make the Cod and Cockles:
While the piperade is cooking, heat 2 tablespoons olive oil in a wide, shallow, lidded saute pan over medium-high heat. Season the cod fillets with salt and pepper; dust the skin sides with the flour.
When oil is hot, add cod, skin-sides down. Cook fish 4 minutes; turn. Add the cockles (or clams), thyme, garlic, parsley leaves, and white wine, arranging the ingredients around the fillets. Cover, and lower heat to medium.
Cook until cockles open, about 5 minutes. (If the cockles or littlenecks haven't opened after 5 minutes, remove the fish and continue cooking until they do.) Uncover the pan, spoon out the fish and clams, and discard the thyme and garlic. Drizzle 1 tablespoon
olive oil over cod. Drizzle 1 tablespoon olive oil into pan and mix with pan juices.
Place the piperade in serving dish. Top with the cod, and surround with the cockles. Spoon the juices around plate; top with chopped parsley, and serve.
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