This is a basic script that will convert a cif file to an in file, already adding the CONTROL, ELECTRON, system parameters and K_points. The only thing left to do is to add the UPF file names in ATOMIC_SPECIES. Cif2Cell is assumed to be installed, it now also has the option to make a supercell.
$chmod +x qeconvert
./qeconvert input.cif output.in
./qeconvert input.cif output.in scalex scaley scalez
./qeconvert input.cif output.in scalex scaley scalez vacuumx vacuumy vacuumz
see ./qeconvert -h
If you forget how to use it, I added a help entry, so just start the program with the -h flag as "qeconvert -h".
Put this file in a directory listed in your path so it can just be called from anywhere like "qeconvert ..."
When making the cif file yourself, you generally don't have an author added, this screws up the formatting a bit (it still works tho)