From 5c57582583f9fab1da11d7bf71385ca5ad8d33d1 Mon Sep 17 00:00:00 2001
From: Yuuki Galaxy <galaxy001@gmail.com>
Date: Wed, 24 Mar 2021 10:52:10 +0800
Subject: [PATCH] 	modified:   tasks/sambamba.wdl

---
 etc/gatk-wdl/fm2/tasks/sambamba.wdl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/etc/gatk-wdl/fm2/tasks/sambamba.wdl b/etc/gatk-wdl/fm2/tasks/sambamba.wdl
index 31167fc26..65600dcef 100644
--- a/etc/gatk-wdl/fm2/tasks/sambamba.wdl
+++ b/etc/gatk-wdl/fm2/tasks/sambamba.wdl
@@ -31,7 +31,7 @@ task Merge {
         Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8) / threads
         String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
     }
-    String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
+    String bamIndexPath = sub(outputPath, "\.bam$", ".csi")
 
     command {
         set -e
@@ -42,7 +42,7 @@ task Merge {
         --write-index \
         ~{outputPath} ~{sep=' ' inputBams}
         # sambamba creates an index for us.
-        mv ~{outputPath}.bai ~{bamIndexPath}
+        mv ~{outputPath}.csi ~{bamIndexPath}
     }
     output {
         File outputBam = outputPath
-- 
2.11.4.GIT