Remove CNNScoreVariants, CNNVariantTrain, and CNNVariantWriteTensors (#9009)

Removed the code for these tools, now that NVScoreVariants is merged
and we've moved to a Python environment that is incompatible with these
legacy tools.

Also added the tools to the DeprecatedToolsRegistry.

Author: droazen

.github/workflows/gatk-tests.yml

@@ -345,12 +345,6 @@ jobs:
           echo "Running M2 WDL";
           bash scripts/m2_cromwell_tests/run_m2_wdl.sh;
 
-      - name: "CNN_WDL_TEST"
-        if: ${{ matrix.wdlTest == 'RUN_CNN_WDL' }}
-        run: |
-          echo "Running CNN WDL";
-          bash scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh;
-
       - name: "VCF_SITE_LEVEL_FILTERING_WDL_TEST"
         if: ${{ matrix.wdlTest == 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' }}
         run: |