From 830eb51555889da4c3733ad5c7bbea4528a57887 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 23 Jul 2020 09:26:14 +0200
Subject: [PATCH] Enable/disable postalt with comment
---
bwa.wdl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index cdaed83..f2c731f 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -46,9 +46,8 @@ task Mem {
Int totalSortThreads = select_first([sortThreads, estimatedSortThreads])
# BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here.
Int estimatedMemoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * totalSortThreads
- String bwaKitCommand = "bwa-postalt.js -p ~{outputPrefix}.hla ~{bwaIndex.fastaFile}" + (if sixtyFour then ".64.alt" else ".alt") + " | "
- String kitCommandString = if usePostalt then bwaKitCommand else ""
+ # The bwa postalt script is out commented as soon as usePostalt = false. It is a hack but it should work.
command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
@@ -59,7 +58,7 @@ task Mem {
~{read1} \
~{read2} \
2> ~{outputPrefix}.log.bwamem | \
- ~{kitCommandString} \
+ ~{true="" false="#" usePostalt} bwa-postalt.js -p ~{outputPrefix}.hla ~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
samtools sort \
~{"-@ " + totalSortThreads} \
-m ~{sortMemoryPerThreadGb}G \
@@ -70,6 +69,7 @@ task Mem {
output {
File outputBam = outputPrefix + ".aln.bam"
+ File? outputHla = outputPrefix + ".hla"
}
runtime {
--
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