From d604025c5d1c603a8a29ce66587f648ebbc4d2d9 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Jun 2020 08:24:24 +0200
Subject: [PATCH] Fix bwakit command
---
bwa.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 4cfd6fb..0c35bf3 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -100,7 +100,7 @@ task Kit {
# BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here.
Int memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * sortThreads
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
- # Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools
+ # Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools 1.10
String dockerImage = "quay.io/biocontainers/mulled-v2-ad317f19f5881324e963f6a6d464d696a2825ab6:c59b7a73c87a9fe81737d5d628e10a3b5807f453-0"
}
@@ -114,7 +114,7 @@ task Kit {
~{read1} \
~{read2} \
2> ~{outputPrefix}.log.bwamem | \
- k8 /opt/conda/bin/bwa-postalt.js \
+ bwa-postalt.js \
-p ~{outputPrefix}.hla \
~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
samtools sort \
--
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