AUTO is AUTO... MANUAL is MANUAL... "Never the twain shall meet!" (Eric Burdon and the Animals)
Single-Cycle is nothing more than a single, complete, iteration of an automatic-multi-cycle process.
Single-Step is nothing more than a single portion of a single cycle of an automatic-multi-cycle process.
Whether or not you can accomplish this depends on the basic design-philosophy in your program.
I recommend... highly modular, with extreme "Flag-Control".
To use "Flag-Control" means to control the initiation of a subsequent Module based on the conditions of the present Module.
The idea of Modularity and Flag-Control is a very involved concept... it takes a lot to explain it... but, once you see it, once you wear it... oh, man...