Fixing bug in the sort portion of MarkDuplicatesAndSort

jonn-smith · jonn-smith · commit 9ee608fe9128 · 2026-01-03T10:22:53.000-05:00
diff --git a/wdl/tasks/Utility/SRUtils.wdl b/wdl/tasks/Utility/SRUtils.wdl
@@ -571,6 +571,7 @@ task MarkDuplicatesAndSort {
         java -jar /usr/picard/picard.jar SortSam \
             INPUT=/dev/stdin \
             OUTPUT=~{prefix}.bam \
+            --SORT_ORDER coordinate \
             CREATE_INDEX=true
     >>>
 
