these should pass the override

broadinstitute · Apr 15, 2022 · ff6a114 · ff6a114
1 parent b772715
commit ff6a114
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/scripts/variantstore/wdl/GvsCreateFilterSet.wdl b/scripts/variantstore/wdl/GvsCreateFilterSet.wdl
@@ -75,7 +75,8 @@ workflow GvsCreateFilterSet {
       ref_fasta = reference,
       ref_fai = reference_index,
       ref_dict = reference_dict,
-      scatter_count = scatter_count
+      scatter_count = scatter_count,
+      gatk_override = gatk_override
   }
 
   scatter(i in range(length(SplitIntervals.interval_files))) {

diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl
@@ -56,6 +56,7 @@ workflow GvsExtractCallset {
       output_gcs_dir = output_gcs_dir,
       split_intervals_disk_size_override = split_intervals_disk_size_override,
       split_intervals_mem_override = split_intervals_mem_override,
+      gatk_override = gatk_override,
       service_account_json_path = service_account_json_path,
   }