Allow the clams soak in cold water for 20 minutes. The clams will release the sand and debris they may be holding. After twenty minutes, you will see the debris at the bottom of the bowl. Next, lift them from the water, scrub them with a stiff brush. Discard any clams that are chipped or not firmly closed.
Swirl olive oil in a heavy bottomed pan over medium heat. Add the shallots and cook until soft and translucent, about 3 to 5 minutes.
Add the sliced garlic and allow to cook until fragrant, about 30 seconds. Do not brown the garlic or it will turn bitter.
Add the white wine and allow to cook for a couple of minutes.
Add the chopped tomatoes.
Add water. Bring to a boil and then reduce heat to a simmer.
Add the salt.
Add the pepper.
Add the thyme.
Add the chili flakes, and then cover and allow to simmer over low heat for about 20 minutes and then taste and adjust seasoning to your liking.
Add the clams to the pot, cover tightly with a lid and allow them to steam for about 3 to 5 minutes or until they have opened. Once the clams have opened, they are done. Remove them from the heat.
Add the lemon zest and sprinkle with fresh chopped Italian flat leaf parsley. GIve the clams a gentle toss and you're ready to serve. Enjoy!