From 7957c85f0e02ebe168262b80720bd1b2881f92e4 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 11 Jun 2018 13:16:20 +0200
Subject: [PATCH] add bam index to ApplyBQSR input

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

diff --git a/gatk.wdl b/gatk.wdl
index dbe4e0c..195627e 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -3,6 +3,7 @@ task ApplyBQSR {
     String? preCommand
     File gatkJar
     File inputBam
+    File inputBamIndex
     String outputBamPath
     File recalibrationReport
     Array[File]+ sequenceGroupInterval
-- 
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