90794159c7cad100f22a85b7f8f1bbb9

Author: SHuang-Broad

wdl/tasks/VariantCalling/DeepVariant.wdl

@@ -59,13 +59,26 @@ workflow Run {
 
         if (shard_id != "alts") {
         if (!use_gpu) {
+            ### shards on t2t that are known to need more memory
             Boolean is_t2t_chrX = length(how_to_shard_wg_for_calling) < 20 && shard_id == "18_X"
             Boolean is_t2t_shard8 = length(how_to_shard_wg_for_calling) < 20 && shard_id == "9_15"
+
+            Boolean is_t2t_pay_toll_shard = is_t2t_chrX || is_t2t_shard8
+
+            ### shards on GRCh38 that are known to need more memory
             Boolean is_38_chr1  = length(how_to_shard_wg_for_calling) > 20 && shard_id == "1-p"
             Boolean is_38_shard3  = length(how_to_shard_wg_for_calling) > 20 && shard_id == "11-q_17-q"
-            Boolean is_38_1q_17p = length(how_to_shard_wg_for_calling) > 20 && shard_id == "1-q_17-p"
 
-            Boolean pay_toll = is_t2t_chrX || is_38_chr1 || is_t2t_shard8 || is_38_shard3 || is_38_1q_17p # true #
+            Boolean is_38_10 = length(how_to_shard_wg_for_calling) > 20 && shard_id == "10"
+            Boolean is_38_13_16p  = length(how_to_shard_wg_for_calling) > 20 && shard_id == "13_16-p"
+            Boolean is_38_21_22_y  = length(how_to_shard_wg_for_calling) > 20 && shard_id == "21_22_y"
+            Boolean is_38_3q_20q  = length(how_to_shard_wg_for_calling) > 20 && shard_id == "3-q_20-q"
+            Boolean is_38_4p_5p_11p  = length(how_to_shard_wg_for_calling) > 20 && shard_id == "4-p_5-p_11-p"
+
+            Boolean is_38_pay_toll_shard = is_38_chr1 || is_38_shard3 || is_38_10 || is_38_13_16p || is_38_21_22_y || is_38_3q_20q || is_38_4p_5p_11p
+
+
+            Boolean pay_toll = is_t2t_pay_toll_shard || is_38_pay_toll_shard # true #
             Int use_this_memory = if (pay_toll) then 6*dv_threads else dv_memory
             call DV as DeepV {
                 input: