How do I make a "Touched" function not take any input until the script stops?

You'll have to use something called debounce. Debounce is basically using a system to ensure that only 1 input is taken while a program is running. To do this, you would have to use a variable, and check whether the variable is a certain value before running the code, like so:

local Active = true
function Test()
	if Active then --Checks to see if the variable "Active" is true
		Active = false --Sets the variable "Active" to false so the code won't run multiple times at once
		--Code
		Active = true --Sets the variable "Active" to true so the code can run again
	end
end

In your case, you would put the code that you have in your function where it says Code, like so:

local Active = true
function touch(hit)
	if Active then
		Active = false
		if hit.Parent ~= nil then
			local player = game.Players:playerFromCharacter(hit.Parent)
			if player ~= nil then
				script.Parent.Parent.first.Transparency = 1
				script.Parent.Parent.first.CanCollide = false
				script.Parent.Parent.second.Transparency = 0
				wait(0.1)
				script.Parent.Parent.second.Transparency = 1
				script.Parent.Parent.second.CanCollide = false
				script.Parent.Parent.third.Transparency = 0
				wait(0.1)
				script.Parent.Parent.third.Transparency = 1
				script.Parent.Parent.third.CanCollide = false
				script.Parent.Parent.fourth.Transparency = 0
				wait(0.1)
				script.Parent.Parent.fourth.Transparency = 1
				script.Parent.Parent.fourth.CanCollide = false
				script.Parent.Parent.fifth.Transparency = 0
				wait(0.1)
				script.Parent.Parent.fifth.Transparency = 1
				script.Parent.Parent.fifth.CanCollide = false
				script.Parent.Parent.sixth.Transparency = 0
				wait(0.1)
				script.Parent.Parent.sixth.Transparency = 1
				script.Parent.Parent.sixth.CanCollide = false
				wait(1) --RESET ROCK--
				script.Parent.Parent.first.Transparency = 0
				script.Parent.Parent.first.CanCollide = true
				
				script.Parent.Parent.second.CanCollide = true
				
				script.Parent.Parent.third.CanCollide = true
				
				script.Parent.Parent.fourth.CanCollide = true
				
				script.Parent.Parent.fifth.CanCollide = true
				
				script.Parent.Parent.sixth.CanCollide = true
			end
		end
		Active = true
	end
end

script.Parent.Touched:connect(touch)

Hope this helped!