Advice / Problems

• not nil doesn't make sense. That' just true. a == not nil does not mean "a is different from nil".
• Don't use == true or == nil ever. Just if something then or if not something then suffices.
  • Don't use elseif when you mean else. Similarly, don't check conditions are the opposite of what they were in the first. That's the point of else and elseif
• Don't mix different types of things together. There's no reason that lightValue should ever be nil. Start at 1.
• Use a name like colors instead of colorTable -- saying "table" doesn't mean anything, it's just a filler word
• Use the names for the BrickColor values. That lets you get rid of the comment -- the code can be understood on its own!

Cleaned-up

After beginning with lightValue = 1 and renaming colorTable to colors, we get this script:

local tower = script.Parent
local lightFolder = tower.Lights
local allLights = lightFolder:GetChildren()

local lightValue = 1
local lightUp = true

colors = {
	BrickColor.new("Pastel yellow"),
	BrickColor.new("Cool yellow"),
	BrickColor.new("Daisy yellow"),
	BrickColor.new("Bright yellow"),
	BrickColor.new("Gold"),
}

while wait(2) do
	if lightUp == true then -- bad! don't say `== true`. `lightUp` on its own is the condition!
		for _, light in pairs(allLights) do
			light.BrickColor = colors[lightValue]
		end
		lightValue = lightValue + 1
		if lightValue == 5 then
			lightUp = false
		end
	elseif lightUp == false then -- bad! we just mean `else`
		for _, light in pairs(allLights) do
			light.BrickColor = colors[lightValue]
		end
		lightValue = lightValue - 1
		if lightValue == 1 then
			lightUp = true
		end
	end
end

Fixing those two conditions,

local tower = script.Parent
local lightFolder = tower.Lights
local allLights = lightFolder:GetChildren()

local lightValue = 1
local lightUp = true

colors = {
	BrickColor.new("Pastel yellow"),
	BrickColor.new("Cool yellow"),
	BrickColor.new("Daisy yellow"),
	BrickColor.new("Bright yellow"),
	BrickColor.new("Gold"),
}

while wait(2) do
	if lightUp then
		for _, light in pairs(allLights) do
			light.BrickColor = colors[lightValue]
		end
		lightValue = lightValue + 1
		if lightValue == 5 then -- bad! magic value.
			lightUp = false
		end
	else
		for _, light in pairs(allLights) do
			light.BrickColor = colors[lightValue]
		end
		lightValue = lightValue - 1
		if lightValue == 1 then
			lightUp = true
		end
	end
end

You have a "magic value" in your code. Why is that 5 as opposed to 4 or 6? In this case, it's the number of colors there are, #colors.

That number is in fact wrong -- you'll be skipping the last. Similarly, == 1 is wrong.

The fixed final version looks like this:

local tower = script.Parent
local lightFolder = tower.Lights
local allLights = lightFolder:GetChildren()

local lightValue = 0
local lightUp = true

colors = {
	BrickColor.new("Pastel yellow"),
	BrickColor.new("Cool yellow"),
	BrickColor.new("Daisy yellow"),
	BrickColor.new("Bright yellow"),
	BrickColor.new("Gold"),
}

while wait(2) do
	if lightUp then
		lightValue = lightValue + 1
		for _, light in pairs(allLights) do
			light.BrickColor = colors[lightValue]
		end
		if lightValue == #colors then
			lightUp = false
		end
	else
		lightValue = lightValue - 1
		for _, light in pairs(allLights) do
			light.BrickColor = colors[lightValue]
		end
		if lightValue == 1 then
			lightUp = true
		end
	end
end

A better start

Clean code reads like prose. You should start describing simply what you want.

You wanted to:

• Show the 1st color
• Show the 2nd
• ...
• Show the last color
• Show the second to last color
• Show the third to last color
• ...
• Show the second color
• Show the first color
• Show the second color
• ...

So here is the code that does exactly that:

function setColor(color)
	for _, light in pairs(allLights) do
		light.BrickColor = color
	end
end

colors = {
	BrickColor.new("Pastel yellow"),
	BrickColor.new("Cool yellow"),
	BrickColor.new("Daisy yellow"),
	BrickColor.new("Bright yellow"),
	BrickColor.new("Gold"),
}

while true do
	wait(2)
	setColor(colors[1])
	wait(2)
	setColor(colors[2])
	wait(2)
	setColor(colors[3])
	wait(2)
	setColor(colors[4])
	wait(2)
	setColor(colors[5])
	wait(2)
	setColor(colors[4])
	wait(2)
	setColor(colors[3])
	wait(2)
	setColor(colors[2])
end

This is shorter than your original code and very clear, but very repetitive. However, it clearly shows the pattern: 1 2 3 4; 5 4 3 2; 1 2 3 4; 5 4 3 2.

This can be easily done with a for loop:

local allLights = lightFolder:GetChildren()

function setColor(color)
	for _, light in pairs(allLights) do
		light.BrickColor = color
	end
end

colors = {
	BrickColor.new("Pastel yellow"),
	BrickColor.new("Cool yellow"),
	BrickColor.new("Daisy yellow"),
	BrickColor.new("Bright yellow"),
	BrickColor.new("Gold"),
}

while true do
	for i = 1, #colors - 1 do
		wait(2)
		setColor(colors[i])
	end
	for i = #colors, 2, -1 do
		wait(2)
		setColor(colors[i])
	end
end

This is much simpler, because it's just doing precisely what you wanted. Don't be clever!