How to target HDF5 datasets as Snakemake input/output?

Question

How can I tell Snakemake that the input/output of a rule should be an HDF5 dataset (so with its own specific "path" within the actual real HDF5 file path)?

Answer 1

snakemake considers the input and output file paths as strings, regardless of the file type and content. If your HDF5 files have a specific path, then use those paths in the input/output directives, possibly using a function-as-input to locate the HDF5 path.

For a more useful answer you should add to your question some example code of what you are trying to do.