From e265f172fdcb2c47d8b4948ed8e9dcdf7fbec298 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 4 Apr 2018 15:08:05 +0200
Subject: [PATCH] runtime adjustments
---
biopet.wdl | 14 ++++++++++----
fastqc.wdl | 8 ++++++--
2 files changed, 16 insertions(+), 6 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 03b1a04..41881e5 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -58,11 +58,14 @@ task SampleConfig {
String? jsonOutputPath
String? tsvOutputPath
+ Float? memory
+ Float? memoryMultiplier
+
command {
set -e -o pipefail
${preCommand}
mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
- java -Xmx3G -jar ${tool_jar} \
+ java -Xmx${default=3 memory}G -jar ${tool_jar} \
-i ${sep="-i " inputFiles} \
${"--sample " + sample} \
${"--library " + library} \
@@ -79,7 +82,7 @@ task SampleConfig {
}
runtime {
- memory: 6
+ memory: selectFirst([memory, 3]) * selectFirst([memoryMultiplier, 1.5])
}
}
@@ -91,11 +94,14 @@ task BaseCounter {
String outputDir
String prefix
+ Float? memory
+ Float? memoryMultiplier
+
command {
set -e -o pipefail
${preCommand}
mkdir -p ${outputDir}
- java -jar ${tool_jar} \
+ java -Xmx${default=12 memory}-jar ${tool_jar} \
-b ${bam} \
-r ${refFlat} \
-o ${outputDir} \
@@ -140,6 +146,6 @@ task BaseCounter {
}
runtime {
- memory: 16
+ memory: selectFirst([memory, 12]) * selectFirst([memoryMultiplier, 1.5])
}
}
diff --git a/fastqc.wdl b/fastqc.wdl
index 7dddd5d..befc4e2 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -62,10 +62,14 @@ task extractAdapters {
File? knownAdapterFile
Float? adapterCutoff
Boolean? outputAsFasta
+
+ Float? memory
+ Float? memoryMultiplier
+
command {
set -e
mkdir -p ${outputDir}
- java -Xmx4G -jar ${extractAdaptersFastqcJar} \
+ java -Xmx${default=4 memory}G -jar ${extractAdaptersFastqcJar} \
--inputFile ${inputFile} \
${"--adapterOutputFile " + adapterOutputFilePath } \
${"--contamsOutputFile " + contamsOutputFilePath } \
@@ -84,7 +88,7 @@ task extractAdapters {
}
runtime {
- memory: 6
+ memory: (if defined(memory) then memory else 4) * (if defined(memoryMultiplier) then memoryMultiplier else 1.5)
}
}
--
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