The Honda CR-Z used to be the only manual transmission hybrid car when it was on sale a few years ago but that model is no longer available. Just about all modern hybrids and EVs have automatic transmissions due to the complex nature of their drivetrains.
Mild hybrids, which incorporate a small 48-volt electric motor with an internal combustion engine, can be paired with manual transmissions and these include models like the Hyundai Tucson MHEV and Kia Stonic MHEV.