From c6eb077f633198a14832ef76497e71a191daaf30 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 24 Jun 2020 15:42:44 +0200
Subject: [PATCH] correct memory calculation
---
bwa.wdl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/bwa.wdl b/bwa.wdl
index 12f2ad5..8d2cb75 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -101,7 +101,7 @@ task Kit {
Int sortMemoryPerThreadGb = 4
Int compressionLevel = 1
# 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 memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * (sortThreads + 1)
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
String dockerImage = "biowdl/bwakit:0.7.17-dev-experimental"
}
--
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