VS-430 Remove YNG status from vds

.dockstore.yml

@@ -155,6 +155,7 @@ workflows:
        branches:
          - master
          - ah_var_store
+         - gg_VS-430_RemoveYNGStatus_From_VDS
        tags:
          - /.*/
    - name: GvsExtractCallset
@@ -308,6 +309,7 @@ workflows:
              - master
              - ah_var_store
              - vs_1396_bq_query_audit
+             - gg_VS-430_RemoveYNGStatus_From_VDS
          tags:
              - /.*/
    - name: GvsIngestTieout

scripts/variantstore/wdl/GvsUtils.wdl

@@ -72,7 +72,7 @@ task GetToolVersions {
     # GVS generally uses the smallest `alpine` version of the Google Cloud SDK as it suffices for most tasks, but
     # there are a handlful of tasks that require the larger GNU libc-based `slim`.
     String cloud_sdk_slim_docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:435.0.0-slim"
-    String variants_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/variants:2024-04-22-alpine-32804b134a75"
+    String variants_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/variants:2024-06-04-alpine-504f661f6b0d"
     String variants_nirvana_docker = "us.gcr.io/broad-dsde-methods/variantstore:nirvana_2022_10_19"
     String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024_05_23-gatkbase-28d855745d35"
     String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest"

scripts/variantstore/wdl/extract/import_gvs.py

@@ -384,6 +384,7 @@ def convert_array_with_id_keys_to_dense_array(arr, ids, drop=[]):
                                                    hl.if_else(is_snp, vd.truth_sensitivity_snp_threshold, vd.truth_sensitivity_indel_threshold),
                                                    True))
             )
+        vd = vd.annotate_rows(as_vqsr=vd.as_vqsr.map_values(lambda value: value.drop('yng_status')))
 
         lgt = vd.LGT
         la = vd.LA