Fix VCF integration assertion, revert extract scatters [VS-1820] (#9340)

Author: mcovarr

.dockstore.yml

@@ -343,7 +343,6 @@ workflows:
          branches:
              - master
              - ah_var_store
-             - vs_1777_build_failure
          tags:
              - /.*/
    - name: GvsIngestTieout

scripts/variantstore/wdl/test/GvsQuickstartIntegration.wdl

@@ -38,7 +38,7 @@ workflow GvsQuickstartIntegration {
     }
 
     String expected_subdir = if (!chr20_X_Y_only) then "all_chrs/"  else ""
-    File expected_output_prefix = "gs://gvs-internal-quickstart/integration/2025-07-21/" + expected_subdir
+    File expected_output_prefix = "gs://gvs-internal-quickstart/integration/2026-03-09/" + expected_subdir
     File truth_data_prefix = "gs://gvs-internal-quickstart/integration/test_data/2025-07-21/" + expected_subdir
 
     # WDL 1.0 trick to set a variable ('none') to be undefined.

scripts/variantstore/wdl/test/GvsQuickstartVcfIntegration.wdl

@@ -444,7 +444,7 @@ task AssertCostIsTrackedAndExpected {
                 DIFF_FOUND=$(echo $EXP_BYTES $OBS_BYTES | awk '{print ($1-$2)/$1}')
               fi
 
-              if ! awk "BEGIN{ exit ($DIFF_FOUND -gt $TOLERANCE) }"
+              if ! awk "BEGIN{ exit ($DIFF_FOUND > $TOLERANCE) }"
               then
                 echo "FAIL!!! The relative difference between these is $DIFF_FOUND, which is greater than the allowed tolerance ($TOLERANCE)"
                 echo "1" > ret_val.txt