expor

broadinstitute · Sep 22, 2022 · d8b7470 · d8b7470
1 parent 79cb502
commit d8b7470
Showing 1 changed file with 30 additions and 0 deletions.
diff --git a/scripts/variantstore/wdl/GvsCallsetStatistics.wdl b/scripts/variantstore/wdl/GvsCallsetStatistics.wdl
@@ -56,6 +56,14 @@ workflow GvsCallsetStatistics {
             aggregate_metrics_table = aggregate_metrics_table,
             statistics_table = statistics_table
     }
+
+    call ExportToTSV {
+        input:
+          project_id = project_id,
+          dataset_name = dataset_name,
+          statistics_table = statistics_table,
+          go = CollectStatistics.done
+    }
 }
 
 task CreateTables {
@@ -718,3 +726,25 @@ task CollectStatistics {
         docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_08_22"
     }
 }
+
+task ExportToTSV {
+    input {
+        String project_id
+        String dataset_name
+        String statistics_table
+        Boolean go
+    }
+    command <<<
+        bq query --nouse_legacy_sql --project_id=~{project_id} --format=csv --field_delimiter=tab '
+
+          SELECT * from `~{project_id}.~{dataset_name}.~{statistics_table}`
+
+        ' > '~{statistics_table}.tsv'
+    >>>
+    output {
+        File tsv = "~{statistics_table}.tsv"
+    }
+    runtime {
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_08_22"
+    }
+}