From 9749968ebb445bd9630940e5e2de478dc12ac220 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 6 Jul 2020 10:26:34 +0200
Subject: [PATCH] Only little memory is needed for gatherbqsrreports
---
gatk.wdl | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index f79312f..0d36e44 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -725,8 +725,8 @@ task GatherBqsrReports {
Array[File] inputBQSRreports
String outputReportPath
- String memory = "1G"
- String javaXmx = "500M"
+ Int memoryMb = 256 + javaXmxMb
+ Int javaXmxMb = 256
Int timeMinutes = 1
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -734,7 +734,7 @@ task GatherBqsrReports {
command {
set -e
mkdir -p "$(dirname ~{outputReportPath})"
- gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
+ gatk --java-options '-Xmx~{javaXmxMb} -XX:ParallelGCThreads=1' \
GatherBQSRReports \
-I ~{sep=' -I ' inputBQSRreports} \
-O ~{outputReportPath}
@@ -747,15 +747,15 @@ task GatherBqsrReports {
runtime {
docker: dockerImage
time_minutes: timeMinutes
- memory: memory
+ memory: "~{memoryMb}M"
}
parameter_meta {
inputBQSRreports: {description: "The BQSR reports to be merged.", category: "required"}
outputReportPath: {description: "The location of the combined BQSR report.", category: "required"}
- memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
--
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