Update GATK Docker image to get required Java 17 JRE

broadinstitute · Jul 18, 2023 · 1b657c2 · 1b657c2
1 parent 9dfd910
commit 1b657c2
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Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/scripts/variantstore/wdl/GvsCreateFilterSet.wdl b/scripts/variantstore/wdl/GvsCreateFilterSet.wdl
@@ -293,7 +293,7 @@ task ExtractFilterTask {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:merge_master_to_ah_var_store_2023_07_18_9b2fbaf"
     memory: "7 GB"
     disks: "local-disk 10 HDD"
     bootDiskSizeGb: 15
@@ -355,7 +355,7 @@ task PopulateFilterSetSites {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:merge_master_to_ah_var_store_2023_07_18_9b2fbaf"
     memory: "3500 MB"
     disks: "local-disk 200 HDD"
     bootDiskSizeGb: 15

diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl
@@ -354,7 +354,7 @@ task ExtractTask {
     echo ~{interval_index},${OUTPUT_FILE_DEST},${OUTPUT_FILE_BYTES},${OUTPUT_FILE_INDEX_DEST},${OUTPUT_FILE_INDEX_BYTES} >> manifest.txt
   >>>
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:merge_master_to_ah_var_store_2023_07_18_9b2fbaf"
     memory: "12 GB"
     disks: "local-disk 150 HDD"
     bootDiskSizeGb: 15

diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl
@@ -121,7 +121,7 @@ workflow GvsImportGenomes {
         load_data_maxretries = effective_load_data_maxretries,
         sample_names = read_lines(CreateFOFNs.vcf_sample_name_fofns[i]),
         sample_map = GetUningestedSampleIds.sample_map,
-        process_vcf_headers = process_vcf_headers
+        process_vcf_headers = process_vcf_headers,
     }
   }
  if (process_vcf_headers) {
@@ -323,7 +323,7 @@ task LoadData {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:merge_master_to_ah_var_store_2023_07_18_9b2fbaf"
     maxRetries: load_data_maxretries
     memory: "3.75 GB"
     disks: "local-disk 50 HDD"

diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl
@@ -41,7 +41,7 @@ task MergeVCFs {
   }
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:merge_master_to_ah_var_store_2023_07_18_9b2fbaf"
     preemptible: select_first([preemptible_tries, 3])
     memory: "3 GiB"
     disks: "local-disk ~{disk_size} HDD"
@@ -127,7 +127,7 @@ task SplitIntervals {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:merge_master_to_ah_var_store_2023_07_18_9b2fbaf"
     bootDiskSizeGb: 15
     memory: "~{disk_memory} GB"
     disks: "local-disk ~{disk_size} HDD"
@@ -918,7 +918,7 @@ task PopulateFilterSetInfo {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:merge_master_to_ah_var_store_2023_07_18_9b2fbaf"
     memory: "3500 MB"
     disks: "local-disk 250 HDD"
     bootDiskSizeGb: 15

diff --git a/scripts/variantstore/wdl/GvsVQSRClassic.wdl b/scripts/variantstore/wdl/GvsVQSRClassic.wdl
@@ -362,7 +362,7 @@ task GatherTranches {
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size + " HDD"
     preemptible: 1
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:merge_master_to_ah_var_store_2023_07_18_9b2fbaf"
   }
 
   output {
@@ -565,7 +565,7 @@ task PopulateFilterSetTranches {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:merge_master_to_ah_var_store_2023_07_18_9b2fbaf"
     memory: "3500 MB"
     disks: "local-disk 200 HDD"
     bootDiskSizeGb: 15