From 0cb76481426e96f75b81a0e1fb516a43e8bffba5 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 24 Jun 2020 10:38:48 +0200
Subject: [PATCH] Revert "Don't sort"
This reverts commit b7d9dad9ad9f804fc41ab8bda3e3961b0441fabc.
---
bwa.wdl | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/bwa.wdl b/bwa.wdl
index 375d8d0..3e11eb2 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -110,7 +110,13 @@ task Kit {
k8 /opt/conda/bin/bwa-postalt.js \
-p ~{outputPrefix}.hla \
~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
- samtools view -b -1 - > ~{outputPrefix}.aln.bam
+ samtools sort \
+ ~{"-@ " + sortThreads} \
+ -m ~{sortMemoryPerThread} \
+ -l ~{compressionLevel} \
+ - \
+ -o ~{outputPrefix}.aln.bam
+ samtools index ~{outputPrefix}.aln.bam ~{outputPrefix}.aln.bai
}
output {
--
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