If the indention is not working, it can be a reason, that the file-ending is not recognized by Atom. Add the support for your language then, for example for "Lua" install the package "language-lua".
If a File is not recognized for your language:
open the ~/.atom/config.cson file (by CTRL+SHIFT+p: type ``open config'')
add/edit a customFileTypes section under core for example like the following: