From ba9bd8935bd8d88bfc234217671aff4934e9149b Mon Sep 17 00:00:00 2001
From: "Thomas B. Mooney" <tmooney@genome.wustl.edu>
Date: Thu, 15 Apr 2021 09:19:01 -0500
Subject: [PATCH] Save the BAM/CRAM index.

---
 WholeGenomeSingleSampleQc.wdl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/WholeGenomeSingleSampleQc.wdl b/WholeGenomeSingleSampleQc.wdl
index 6e8278e..5f5b2cf 100644
--- a/WholeGenomeSingleSampleQc.wdl
+++ b/WholeGenomeSingleSampleQc.wdl
@@ -171,5 +171,6 @@ workflow SingleSampleQc {
     File? hs_metrics = CollectHsMetrics.metrics
 
     File input_bam_md5 = CalculateChecksum.md5
+    File input_bam_index = BuildBamIndex.bam_index
   }
 }