Follow up on CNN deprecation done in the update to python 3.10.

[samuelklee]

After the updates to the python environment made in #8561, the CNN tools are no longer functional and were deprecated.

However, we may want to provide a separate environment in which some of these tools can still be used, perhaps in conjunction with NVScoreVariants. If so, we should also re-enable the relevant integration and WDL tests and provide appropriate documentation.