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broadinstitute · May 16, 2022 · 0ff2f76 · 0ff2f76
1 parent 9e65874
commit 0ff2f76
Showing 1 changed file with 7 additions and 4 deletions.
diff --git a/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl b/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl
@@ -123,10 +123,10 @@ workflow GvsValidateVat {
 
     call SpotCheckForAAChangeAndExonNumberConsistency {
          input:
-         query_project_id = query_project_id,
-         fq_vat_table = fq_vat_table,
-        service_account_json_path = service_account_json_path,
-        last_modified_timestamp = GetBQTableLastModifiedDatetime.last_modified_timestamp
+            query_project_id = query_project_id,
+            fq_vat_table = fq_vat_table,
+            service_account_json_path = service_account_json_path,
+            last_modified_timestamp = GetBQTableLastModifiedDatetime.last_modified_timestamp
     }
 
     output {
@@ -235,6 +235,7 @@ task EnsureVatTableHasVariants {
         # otherwise, something is off, so return the output from the bq query call
         else
             echo "Something went wrong. The attempt to count the variants returned: " $(cat bq_variant_count.csv) > validation_results.txt
+            exit 1
         fi
     >>>
     # ------------------------------------------------
@@ -1004,6 +1005,7 @@ task SchemaAAChangeAndExonNumberConsistent {
         # otherwise, something is off, so return the output from the bq query call
         else
             echo "Something went wrong. The attempt to count the variants returned: " $(cat bq_aachange_exonnumber.csv) > validation_results.txt
+            exit 1
         fi
     >>>
     # ------------------------------------------------
@@ -1115,6 +1117,7 @@ task SpotCheckForAAChangeAndExonNumberConsistency {
         # otherwise, something is off, so return the output from the bq query call
         else
             echo "Something went wrong. The attempt to count the spot checked entries returned: " $(cat output.csv.csv) > validation_results.txt
+            exit 1
         fi
     >>>