modify maximum_cycle_value parameter

broadinstitute · Jul 26, 2024 · ec352ec · ec352ec
1 parent da7737c
commit ec352ec
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/wdl/tasks/Utility/SRUtils.wdl b/wdl/tasks/Utility/SRUtils.wdl
@@ -399,6 +399,7 @@ task BaseRecalibrator {
         File known_sites_index
 
         String prefix
+        Int maximum_cycle_value = 1000
 
         RuntimeAttr? runtime_attr_override
     }
@@ -425,7 +426,9 @@ task BaseRecalibrator {
             -I ~{input_bam} \
             --use-original-qualities \
             -O ~{prefix}.txt \
-            --known-sites ~{known_sites_vcf}
+            --known-sites ~{known_sites_vcf} \
+            --maximum-cycle-value ~{maximum_cycle_value} 
+
 
     }
     #########################