Ghost In The Machine: Averted. Souls are software objects; there are no supernatural qualities whatsoever to sophont life, and even if you can pull out the software, recompile it, and stick it in another body, the only thing that’s being transferred is data.
It would always be possible to consider the logos/personality organization algorithm, the weird non-deterministic chunk of mathematics that appears to produce volition as something of this sort, I suppose; or in a weak Cartesian-theater sense the consciousness loop, even if all it does is organize your cognitive processing into a narrative thread, and it’s entirely possible to build minds without them if you’re okay with the resulting weirdness. But in no case is there any ghost present; it’s just the “program in the machine”.
(That all being said, of course, when asked geth-type questions like “Does this unit have a soul?”, the Imperial answer is unambiguously yes. Inasmuch as “soul”, in modern sophotechnologist jargon, is slang for “personality organization algorithm”, which is to say, that thing which makes you you.)