For this pasta dish, you may serve the clams in their shells, with a bowl on the table to collect them. Or, if you prefer, you can remove them beforehand.
Bring a large pot of salted water to a boil, and cook pasta until just al dente. Drain.
Meanwhile, heat oil in a large skillet over medium-high heat. Add garlic, shallot, Cubanelle pepper, and red-pepper flakes; saute until translucent, about 4 minutes. Add wine; bring to a boil, scraping up browned bits. Add clam juice; return to a boil. Add clams, cover, and cook just until they open, about 5 minutes (start checking after 4 minutes, and discard any clams that have not opened after 6 minutes).
Add linguine, tossing with tongs to combine with clams. Season with salt if necessary (depending on saltiness of clams), remove from heat, and add parsley. Serve immediately.