UNIX provides the Makefile as go-to tool if a simple pipeline is not enough. GNUmake makes this even more powerful by being able to generate rules on-the-fly.
If the tool of interest works with files (like the UNIX tools do) it fits very well.
If the tool doesn't work with single files I have had some success in using Makefiles for generic processing tasks by creating a marker file that a given task was complete as part of the target.