From 38b1c5f1369a8ae035a06a2b4f78eb7f6b9f97ec Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 5 Apr 2018 10:36:15 +0200
Subject: [PATCH] adjust memory
---
biopet.wdl | 4 ++--
fastqc.wdl | 4 ++--
picard.wdl | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 9d1a319..2eb2988 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -65,7 +65,7 @@ task SampleConfig {
set -e -o pipefail
${preCommand}
mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
- java -Xmx${true=""+memory false="4" defined(memory)}G -jar ${tool_jar} \
+ java -Xmx${true=memory false="4" defined(memory)}G -jar ${tool_jar} \
-i ${sep="-i " inputFiles} \
${"--sample " + sample} \
${"--library " + library} \
@@ -101,7 +101,7 @@ task BaseCounter {
set -e -o pipefail
${preCommand}
mkdir -p ${outputDir}
- java -Xmx${true=""+memory false="12" defined(memory)}G -jar ${tool_jar} \
+ java -Xmx${true=memory false="12" defined(memory)}G -jar ${tool_jar} \
-b ${bam} \
-r ${refFlat} \
-o ${outputDir} \
diff --git a/fastqc.wdl b/fastqc.wdl
index 968c4a4..1b1296d 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -70,7 +70,7 @@ task extractAdapters {
command {
set -e
mkdir -p ${outputDir}
- java -Xmx${true=""+memory false="4" defined(memory)}G -jar ${extractAdaptersFastqcJar} \
+ java -Xmx${true=memory false="4" defined(memory)}G -jar ${extractAdaptersFastqcJar} \
--inputFile ${inputFile} \
${"--adapterOutputFile " + adapterOutputFilePath } \
${"--contamsOutputFile " + contamsOutputFilePath } \
@@ -89,7 +89,7 @@ task extractAdapters {
}
runtime {
- memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 2.0]))
+ memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 2.5]))
}
}
diff --git a/picard.wdl b/picard.wdl
index d394ee0..4015751 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -90,7 +90,7 @@ task MarkDuplicates {
${preCommand}
mkdir -p $(dirname ${output_bam_path})
java ${"-Dsamjdk.compression_level=" + compression_level} \
- -Xmx${true=memory false="4" defined(memory)}G -jar ${picard_jar} \
+ -Xmx${true=memory false="8" defined(memory)}G -jar ${picard_jar} \
MarkDuplicates \
INPUT=${sep=' INPUT=' input_bams} \
OUTPUT=${output_bam_path} \
@@ -110,7 +110,7 @@ task MarkDuplicates {
}
runtime {
- memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
+ memory: ceil(select_first([memory, 8.0]) * select_first([memoryMultiplier, 1.5]))
}
}
--
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