From 7252022d6ab47c58962ae330ffea273056f3560e Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 26 Jun 2020 14:21:07 +0200
Subject: [PATCH] sambamba creates index automaticall
---
sambamba.wdl | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sambamba.wdl b/sambamba.wdl
index b402f58..4de4dfd 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -94,9 +94,8 @@ task Sort {
-m ~{memoryPerThreadGb}G \
-o ~{outputPath} \
~{inputBam}
- sambamba index \
- ~{"--nthreads " + threads} \
- ~{outputPath} ~{bamIndexPath}
+ # sambamba creates an index for us
+ mv ~{outputPath}.bai ~{bamIndexPath}
}
output {
--
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