From bf6145791588577ee502749a7662f0683e67aab9 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 5 Jun 2020 07:56:50 +0200
Subject: [PATCH] try to fix memory
---
star.wdl | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/star.wdl b/star.wdl
index b1c662f..f154913 100644
--- a/star.wdl
+++ b/star.wdl
@@ -104,7 +104,9 @@ task Star {
Int runThreadN = 4
# Use a margin of 30% index size. Real memory usage is ~30 GiB for a 27 GiB index.
Int memoryGb = 1 + ceil(size(indexFiles, "G") * 1.3)
- String memory = "~{memoryGb}G"
+ # For some reason doing above calculation inside a string does not work.
+ # So we solve it with an optional memory string and using select_first.
+ String? memory
# 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"
@@ -137,7 +139,7 @@ task Star {
runtime {
cpu: runThreadN
- memory: memory
+ memory: select_first([memory, "~{memoryGb}G"])
time_minutes: timeMinutes
docker: dockerImage
}
--
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