The specs for your functions seem to be valid, dialyzer complains about the calls.
x = from …
y = x
|> function1()
|> function2()
|> limit(10)
function3(y)
will probably be fine.
Unless you are running the query in function3/1, you can also swap the ordering:
x = from …
x
|> function1()
|> function2()
|> function3()
|> limit(10)
