Merge branch 'master' into kj_sv_cleanvcf

broadinstitute · Oct 18, 2024 · 354857f · 354857f
2 parents 74de1b0 + b409f77
commit 354857f
Show file tree

Hide file tree

Showing 88 changed files with 3,175 additions and 6,500 deletions.
diff --git a/.github/workflows/gatk-tests.yml b/.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: |

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-ARG BASE_DOCKER=broadinstitute/gatk:gatkbase-3.3.0
+ARG BASE_DOCKER=broadinstitute/gatk:gatkbase-3.3.1
 
 # stage 1 for constructing the GATK zip
 FROM ${BASE_DOCKER} AS gradleBuild