I've tried a few other techniques, but there is something that is really hard to beat about the plain Makefile. Eventually, it can become unwieldy, but for small-medium projects, it's a life saver. Combine that with git, and you've got a pretty robust system. The only real downside is that when you have very large initial inputs, it isn't practical to store those in the same repository.

That is my goto combinations for bioinformatics workflows that don't need to run on a cluster. (A Makefile variant of mine is my go-to for clusters). I've experimented with Docker workflows, which while in theory are nice, you'll always require some sort of organizing script to document the analysis. (Docker is still nice for capturing program versioning/configuration though!)