From 0b1579589376f1fe95472e9d68b2109e25f00496 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 8 Feb 2018 16:34:30 +0100
Subject: [PATCH] also give index
---
bwa.wdl | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/bwa.wdl b/bwa.wdl
index 4d9aad1..b7762f2 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -88,7 +88,8 @@ task mem {
INPUT=/dev/stdin SORT_ORDER=coordinate OUTPUT=${outputFile}
}
output {
- File alignedFile = select_first([outputFile])
+ File bamFile = select_first([outputFile])
+ File bamIndex = sub(bamFile, ".bam$", ".bai")
}
runtime {
cpu: select_first([threads])
--
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