VS-1470 Have Extract Cohort to PGEN write to cost_observability table (…

…#8958) * Have ExtractCohortToPgen write to cost_observability table.
broadinstitute · Aug 21, 2024 · 35601a1 · 35601a1
1 parent 48f4bf5
commit 35601a1
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diff --git a/scripts/variantstore/wdl/GvsExtractCallsetPgen.wdl b/scripts/variantstore/wdl/GvsExtractCallsetPgen.wdl
@@ -441,7 +441,7 @@ task PgenExtractTask {
                 ${FILTERING_ARGS} \
                 --dataset-id ~{dataset_name} \
                 --call-set-identifier ~{call_set_identifier} \
-                --wdl-step GvsExtractCallsetPgenPgen \
+                --wdl-step GvsExtractCallsetPgen \
                 --wdl-call PgenExtractTask \
                 --shard-identifier ~{interval_filename} \
                 ~{cost_observability_line} \

diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/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:2024-08-15-alpine-254df9be288d"
     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_08_08-gatkbase-7dc245ec27ce"
+    String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024_08_19-gatkbase-cd5b6b7821b2"
     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"

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortToPgen.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortToPgen.java
@@ -211,7 +211,8 @@ protected void apply(VariantContext variantContext) {
 
     @Override
     public Object onTraversalSuccess() {
-        if(pgenWriter.getDroppedVariantCount() > 0l) {
+        super.onTraversalSuccess();
+        if (pgenWriter.getDroppedVariantCount() > 0l) {
             logger.info(pgenWriter.getDroppedVariantCount() + " variants dropped by writer for exceeding the" +
                     " maximum number of allowed alt alleles.");
         }