From 00fd8d40a7680913c578e43b49770b30838656bb Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 9 Feb 2018 12:09:43 +0100
Subject: [PATCH] solved indexing issue
---
bwa.wdl | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index b7762f2..fb222ad 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -70,7 +70,6 @@ task mem {
${true="-p " false="" smartPairing} \
${"-r " + readGroupHeaderLine} \
${"-H " + H } \
- ${"-o " + outputFile } \
${true="-j" false="" j } \
${true="-5" false="" five } \
${true="-q" false="" q } \
@@ -86,10 +85,12 @@ task mem {
${indexBase} ${read1} ${read2} \
| picard SortSam CREATE_INDEX=TRUE TMP_DIR=null \
INPUT=/dev/stdin SORT_ORDER=coordinate OUTPUT=${outputFile}
+ ln -s $(basename ${outputFile} | sed 's/.bam$/.bai/') ${outputFile}.bai
}
output {
File bamFile = select_first([outputFile])
- File bamIndex = sub(bamFile, ".bam$", ".bai")
+ File bamIndexPicard = sub(bamFile, ".bam$", ".bai")
+ File bamIndexSamtools = select_first([outputFile]) + ".bai"
}
runtime {
cpu: select_first([threads])
--
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