Extract Cohort optimizations [VS-493] [VS-1516] (#9055)

* wip

* more dropping, more logging

* gah

* Docker

* yolo

* Docker

* Docker

* minor fixes, not worth rebuilding Docker

* minor updates

* Docker

* begin additional restructuring

* cleanup of existing code

* Docker

* Docker

* windowing comments wip

* windowing comments

.dockstore.yml

@@ -173,6 +173,7 @@ workflows:
          branches:
              - master
              - ah_var_store
+             - vs_1516_yolo
          tags:
              - /.*/
    - name: GvsImportGenomes
@@ -241,6 +242,7 @@ workflows:
          branches:
              - master
              - ah_var_store
+             - vs_1516_yolo
          tags:
              - /.*/
    - name: GvsWithdrawSamples
@@ -314,7 +316,7 @@ workflows:
          branches:
              - master
              - ah_var_store
-             - vs_1490_fix_curate_input_array_files
+             - vs_1516_yolo
          tags:
              - /.*/
    - name: GvsIngestTieout

scripts/variantstore/wdl/GvsUtils.wdl

@@ -74,7 +74,7 @@ task GetToolVersions {
     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:2024-11-25-alpine-913039adf8f4"
     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:2024-11-24-gatkbase-1807487d5912"
+    String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024-11-28-gatkbase-b71132a18899"
     String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest"
     String gotc_imputation_docker = "us.gcr.io/broad-gotc-prod/imputation-bcf-vcf:1.0.5-1.10.2-0.1.16-1649948623"
     String plink_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/plink2:2024-04-23-slim-a0a65f52cc0e"