From b02601ad09eb75f2a3fdd92de2e4f94e2b418f28 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 4 Apr 2018 15:53:25 +0200
Subject: [PATCH] fix default memory?
---
biopet.wdl | 4 ++--
fastqc.wdl | 3 ++-
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 554c754..cdfdff7 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${default=3.0 memory}G -jar ${tool_jar} \
+ java -Xmx${true=""+memory false="3" 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 ${outputDir}
- java -Xmx${default=12.0 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 12b481e..aa9073e 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -66,10 +66,11 @@ task extractAdapters {
Float? memory
Float? memoryMultiplier
+
command {
set -e
mkdir -p ${outputDir}
- java -Xmx${default=4.0 memory}G -jar ${extractAdaptersFastqcJar} \
+ java -Xmx$${true=""+memory false="4" defined(memory)}G -jar ${extractAdaptersFastqcJar} \
--inputFile ${inputFile} \
${"--adapterOutputFile " + adapterOutputFilePath } \
${"--contamsOutputFile " + contamsOutputFilePath } \
--
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