From 09772e613aaf6d9029de629b9585e060bcfd1d2d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 6 Jul 2020 10:28:05 +0200
Subject: [PATCH] Comment on real life use for sambamba markdup
---
sambamba.wdl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sambamba.wdl b/sambamba.wdl
index bf58dbc..cd8da21 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -37,7 +37,7 @@ task Markdup {
Boolean removeDuplicates = false
# According to the manual sambamba markdup uses the sortbufferSize + 2 times the ioBuffer size.
- # Added 1024 mb as a margin of safety
+ # Added 1024 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
Int memoryMb = 1024 + sortBufferSize + 2 * ioBufferSize
String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
# Time minute calculation does not work well for higher number of threads.
--
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