From 05a55103f65c2ebb308a0f3e7d1545b21c28dba2 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 31 Jan 2018 11:35:30 +0100
Subject: [PATCH] output as sorted and indexed bam
---
bwa.wdl | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 04320ad..6cd0cda 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -2,7 +2,7 @@ task mem {
File read1
File referenceFile
File? read2
- String? outputFile
+ String? outputFile = "aligned.bam"
String? preCommand
Int? threads = 1
String? memory = "4G"
@@ -78,10 +78,12 @@ task mem {
${true="-Y" false="" Y } \
${true="-M" false="" M } \
${"-I " + I } \
- ${referenceFile} ${read1} ${read2}
+ ${referenceFile} ${read1} ${read2} \
+ | picard SortSam CREATE_INDEX=TRUE TMP_DIR=null \
+ INPUT=/dev/stdin OUTPUT=${outputFile}
}
output {
- File samFile = if defined(outputFile) then select_first([outputFile]) else stdout()
+ File samFile = select_first([outputFile])
}
runtime {
cpu: select_first([threads])
--
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