From 3261563d3d5f873a062dc190f6e1c18846916f76 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 4 Jun 2020 13:41:26 +0200
Subject: [PATCH] Tune memory and time requirements for RNA seq
---
star.wdl | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/star.wdl b/star.wdl
index c262dc5..4b204eb 100644
--- a/star.wdl
+++ b/star.wdl
@@ -102,9 +102,10 @@ task Star {
Int? limitBAMsortRAM
Int runThreadN = 4
- String memory = "~{5 + ceil(size(indexFiles, "G"))}G"
- # 1 minute initialization + time reading in index + time aligning data.
- Int timeMinutes = 1 + ceil(size(indexFiles, "G") / 2) + ceil(size(flatten([inputR1, inputR2]), "G") * 180 / runThreadN)
+ # Use a margin of 30% index size. Real memory usage is ~30 GiB for a 27 GiB index.
+ String memory = "~{1 + ceil(size(indexFiles, "G") * 1.3)}G"
+ # 1 minute initialization + time reading in index (1 minute per G) + time aligning data.
+ Int timeMinutes = 1 + ceil(size(indexFiles, "G")) + ceil(size(flatten([inputR1, inputR2]), "G") * 180 / runThreadN)
String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
}
--
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