I agree with the OP: The (most reasonable) design process consists of first identifying the functional (i.e. language-independent) algorithm that solves the problem in the theoretically most appropriate way.

After that, modules may well exist to fill in some of the coding requirements, but it is often wrong to use a module which misses the mark even slightly. For example, if a module can do everything with a set a files except just one of the things you need, it might be hard to justify doubling the number of passes through all the files just to use the module for most of the requirements, especially if there are hundreds of files adding up to several gigabytes of data to be processed.