From fec7883af9502f9c2b090856857c91f90eb799c9 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 5 Apr 2018 11:55:22 +0200
Subject: [PATCH] add runtime to scatterRegions
---
biopet.wdl | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/biopet.wdl b/biopet.wdl
index 2eb2988..3ae5490 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -32,11 +32,14 @@ task ScatterRegions {
Int? scatterSize
File? regions
+ Float? memory
+ Float? memoryMultiplier
+
command {
set -e -o pipefail
${preCommand}
mkdir -p ${outputDirPath}
- java -Xmx2G -jar ${tool_jar} \
+ java -Xmx${true=memory false="2" defined(memory)}G -jar ${tool_jar} \
-R ${ref_fasta} \
-o ${outputDirPath} \
${"-s " + scatterSize} \
@@ -46,6 +49,10 @@ task ScatterRegions {
output {
Array[File] scatters = glob(outputDirPath + "/scatter-*.bed")
}
+
+ runtime {
+ memory: ceil(select_first([memory, 2.0]) * select_first([memoryMultiplier, 2.0]))
+ }
}
task SampleConfig {
--
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