From 9f2940e0961c70841a61e0ec292e37b5f1d7c396 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 20 Mar 2015 15:04:54 +0100
Subject: [PATCH] Change limits to coreMemory
---
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala | 2 +-
.../sasc/biopet/extensions/RscriptCommandLineFunction.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala | 2 +-
.../sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala | 2 +-
.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala | 3 +--
.../nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala | 2 +-
.../sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala | 3 +--
.../main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala | 3 +--
.../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala | 3 +--
.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala | 3 +--
.../main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala | 3 +--
.../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala | 3 +--
.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala | 3 +--
.../main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala | 3 +--
.../src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala | 3 +--
.../src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala | 3 +--
.../main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala | 3 +--
.../scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala | 3 +--
.../scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala | 3 +--
.../src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala | 3 +--
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala | 3 +--
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala | 3 +--
38 files changed, 38 insertions(+), 55 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index b7fd54634..ac30b3b32 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -44,7 +44,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
override val versionExitcode = List(0, 1)
override def versionCommand = executable + " --version"
- override val defaultVmem = "6G"
+ override val defaultCoreMemory = 4.0
override val defaultThreads = 8
var sam: Boolean = config("sam", default = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
index 9658701d7..b252d9c9e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
@@ -33,7 +33,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 8
/** default vmem for cluster jobs */
- override val defaultVmem = "8G"
+ override val defaultCoreMemory = 6.0
/** input file */
@Input(doc = "Input file (SAM or BAM)", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
index ad949c7d2..b002adf5a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
@@ -35,7 +35,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 8
/** default vmem for cluster jobs */
- override val defaultVmem = "16G"
+ override val defaultCoreMemory = 10.0
/** input file */
@Input(doc = "Input FASTQ file(s)", required = true) //var input: List[File] = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
index 6756c5eaf..830e72df7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
@@ -33,7 +33,7 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
var decomrpess = true
var memory: Option[Int] = config("memory")
- override val defaultVmem = (memory.getOrElse(1000) * 2 / 1000) + "G"
+ override val defaultCoreMemory = memory.getOrElse(1000).toDouble / 1000
override val defaultThreads = 2
override def beforeCmd {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
index 61e4d06dd..a1935a776 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
@@ -36,7 +36,7 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
protected var script: File = _
protected var scriptName: String = _
protected var arguments: ListBuffer[String] = ListBuffer()
- override val defaultVmem: String = "4G"
+ override val defaultCoreMemory = 2.0
executable = config("exe", default = "Rscript", submodule = "R")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
index a9cbbd668..daea56de8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
@@ -64,7 +64,7 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
override val versionExitcode = List(0, 1)
/// Stampy uses approx factor 1.1 times the size of the genome in memory.
- override val defaultVmem = "4G"
+ override val defaultCoreMemory = 4.0
override val defaultThreads = 8
override def versionCommand = executable + " --help"
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index e75307262..2a8738e5f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -63,7 +63,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
var outFileNamePrefix: String = _
var runThreadN: Option[Int] = config("runThreadN")
- override val defaultVmem = "6G"
+ override val defaultCoreMemory = 4.0
override val defaultThreads = 8
/** Sets output files for the graph */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
index f0d7944aa..d4103a5b2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
@@ -32,7 +32,7 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
override val versionExitcode = List(0, 1)
override def versionCommand = executable + " --version"
- override val defaultVmem = "6G"
+ override val defaultCoreMemory = 4.0
override val defaultThreads = 8
@Input(doc = "FastQ file(s) R1", shortName = "R1")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
index caab2715e..b84ebb49f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
@@ -46,7 +46,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
if (input.getName.endsWith(".bam")) inputTag = "-abam"
}
- override val defaultVmem = "6G"
+ override val defaultCoreMemory = 4.0
/** Returns command to execute */
def cmdLine = required(executable) + required("coverage") +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
index fc488e901..117296835 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
@@ -60,7 +60,7 @@ class BwaAln(val root: Configurable) extends Bwa {
var n2: Boolean = config("2", default = false)
var Y: Boolean = config("Y", default = false)
- override val defaultVmem = "5G"
+ override val defaultCoreMemory = 4.0
override val defaultThreads = 8
/** Returns command to execute */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index 70e922c7c..285e31435 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -69,7 +69,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var Y: Boolean = config("Y", default = false)
var I: Option[String] = config("I")
- override val defaultVmem = "6G"
+ override val defaultCoreMemory = 4.0
override val defaultThreads = 8
def cmdLine = {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
index 79fadce17..40a545856 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
@@ -26,7 +26,7 @@ abstract class Conifer extends PythonCommandLineFunction {
override val versionExitcode = List(0)
override def versionCommand = executable + " " + python_script + " --version"
- override val defaultVmem = "8G"
+ override val defaultCoreMemory = 5.0
override val defaultThreads = 1
def cmdLine = getPythonCommand
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
index 799b05bb4..27ca1bdea 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
@@ -31,7 +31,7 @@ abstract class Gatk extends BiopetJavaCommandLineFunction {
val analysisType: String
- override val defaultVmem = "5G"
+ override val defaultCoreMemory = 3.0
@Input(required = true)
var reference: File = config("reference")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
index 401510088..28e1502fe 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
@@ -59,7 +59,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var pairs: Boolean = config("pairs", default = false)
- override val defaultVmem = "6G"
+ override val defaultCoreMemory = 4.0
override def beforeGraph {
super.beforeGraph
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index b45334eb9..d0ad79666 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -60,8 +60,7 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0, 1)
- override val defaultVmem = "8G"
- memoryLimit = Option(3.0)
+ override val defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
required("TMP_DIR=" + jobTempDir) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
index a2804668e..de2b93ee8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/** General Sambamba extension */
abstract class Sambamba extends BiopetCommandLineFunction {
- override val defaultVmem = "4G"
+ override val defaultCoreMemory = 2.0
override val defaultThreads = 2
override def subPath = "sambamba" :: super.subPath
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
index 2ded76dc8..7f35bc1af 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
@@ -84,7 +84,7 @@ object BreakdancerConfig {
class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "breakdancer-max", freeVar = false)
- override val defaultVmem = "6G"
+ override val defaultCoreMemory = 4.0
override val defaultThreads = 1 // breakdancer can only work on 1 single thread
override val versionRegex = """.*[Vv]ersion:? (.*)""".r
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala
index d06a1811b..ec0452af8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala
@@ -28,7 +28,7 @@ class Clever(val root: Configurable) extends BiopetCommandLineFunction {
private lazy val versionexecutable: File = config("version_exe", default = (new File(executable).getParent + "/ctk-version"))
- override val defaultVmem = "4G"
+ override val defaultCoreMemory = 3.0
override val defaultThreads = 8
override def versionCommand = versionexecutable.getAbsolutePath
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala
index 6bcc62033..02bcc19a8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala
@@ -23,7 +23,7 @@ import java.io.File
class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "pindel", freeVar = false)
- override val defaultVmem = "8G"
+ override val defaultCoreMemory = 5.0
override val defaultThreads = 8
override val versionRegex = """Pindel version:? (.*)""".r
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
index bd152a383..2889e0581 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
@@ -29,7 +29,6 @@ abstract class Varscan extends BiopetJavaCommandLineFunction {
* override val versionRegex = """VarScan v(.*)""".r
*/
- override val defaultVmem = "8G"
- memoryLimit = Option(3.0)
+ override val defaultCoreMemory = 5.0
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
index 80704ef77..cf3485038 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
@@ -32,7 +32,7 @@ class CoverageStats(val root: Configurable) extends PythonCommandLineFunction {
@Output(doc = "plot File (png)")
var plot: File = _
- override val defaultVmem = "12G"
+ override val defaultCoreMemory = 9.0
def cmdLine = getPythonCommand +
required(input) + required("--plot", plot) + " > " + required(output)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index 188e8f824..8f9f3155a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -56,8 +56,7 @@ class BastyGenerateFasta(val root: Configurable) extends BiopetJavaCommandLineFu
var minDepth: Int = config("min_depth", default = 8)
var outputName: String = _
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
+ override val defaultCoreMemory = 4.0
override def commandLine = super.commandLine +
optional("--inputVcf", inputVcf) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
index 55b13c542..58b9500ad 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
@@ -36,8 +36,7 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio
@Output(doc = "Output interval list", required = true)
var output: File = _
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
+ override val defaultCoreMemory = 1.0
override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
index 0f7a922b0..6502f46c2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
@@ -35,8 +35,7 @@ class BedtoolsCoverageToCounts(val root: Configurable) extends BiopetJavaCommand
@Output(doc = "Output tag library", shortName = "output", required = true)
var output: File = _
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
+ override val defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
required("-I", input) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
index fdc06dd9f..f72ea06d5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
@@ -37,8 +37,7 @@ class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFuncti
@Output(doc = "summary output file", shortName = "output", required = false)
var summaryFile: File = _
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
+ override val defaultCoreMemory = 2.0
override def commandLine = super.commandLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
index 61c76085f..4a034e2e5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
@@ -36,8 +36,7 @@ class FastqSplitter(val root: Configurable) extends BiopetJavaCommandLineFunctio
@Output(doc = "Output fastq files", shortName = "output", required = true)
var output: List[File] = Nil
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
+ override val defaultCoreMemory = 1.0
/**
* Generate command to execute
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index 004fba431..ad99cbafa 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -57,8 +57,7 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction wi
@Output(doc = "Sync statistics", required = true)
var outputStats: File = null
- override val defaultVmem = "4G"
- memoryLimit = Some(1.7)
+ override val defaultCoreMemory = 2.0
// executed command line
override def commandLine =
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index 3eec803c8..8d3b6358f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -46,8 +46,7 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction
var reference: File = config("reference")
- override val defaultVmem = "8G"
- memoryLimit = Option(4)
+ override val defaultCoreMemory = 1.0
override def beforeGraph {
super.beforeGraph
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
index 6dca83472..b21a15f97 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
@@ -28,7 +28,7 @@ class MergeTables(val root: Configurable) extends BiopetJavaCommandLineFunction
javaMainClass = getClass.getName
- override val defaultVmem = "5G"
+ override val defaultCoreMemory = 2.0
@Input(doc = "Input table files", required = true)
var inputTables: List[File] = List.empty[File]
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index a89e6a851..e33e64f1e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -49,8 +49,7 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
var sample: String = _
var reference: String = config("reference")
- override val defaultVmem = "6G"
- memoryLimit = Option(2.0)
+ override val defaultCoreMemory = 3.0
override def defaults = ConfigUtils.mergeMaps(Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1)),
super.defaults)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
index ac15749eb..6dfc15221 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
@@ -31,8 +31,7 @@ import scala.collection.JavaConversions._
class PrefixFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
- memoryLimit = Some(1.0)
- override val defaultVmem = "4G"
+ override val defaultCoreMemory = 1.0
@Input(doc = "Input fastq", shortName = "I", required = true)
var inputFastq: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
index a3475d26a..464346feb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
@@ -36,8 +36,7 @@ class SageCountFastq(val root: Configurable) extends BiopetJavaCommandLineFuncti
@Output(doc = "Output tag library", shortName = "output", required = true)
var output: File = _
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
+ override val defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
required("-I", input) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
index e8803863a..3f5af4439 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
@@ -49,8 +49,7 @@ class SageCreateLibrary(val root: Configurable) extends BiopetJavaCommandLineFun
var tag: String = config("tag", default = "CATG")
var length: Option[Int] = config("length", default = 17)
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
+ override val defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
required("-I", input) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
index 7c4256d72..075b90f44 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
@@ -46,8 +46,7 @@ class SageCreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineF
@Output(doc = "AntiSense all count file", shortName = "allantisense", required = true)
var countAllAntiSense: File = _
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
+ override val defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
required("-I", input) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
index d4f2918dd..66822401b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
@@ -48,8 +48,7 @@ class Seqstat(val root: Configurable) extends BiopetJavaCommandLineFunction with
@Output(doc = "Output JSON", shortName = "output", required = true)
var output: File = null
- override val defaultVmem = "3G"
- memoryLimit = Option(1.0)
+ override val defaultCoreMemory = 1.0
override def commandLine = super.commandLine + required("-i", input) + " > " + required(output)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index 76f8887cc..32cf5d42e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
@@ -43,8 +43,7 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
var minSamplesPass: Option[Int] = config("min_samples_pass")
var filterRefCalls: Boolean = config("filter_ref_calls", default = false)
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
+ override val defaultCoreMemory = 1.0
override def commandLine = super.commandLine +
required("-I", inputVcf) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index a60a5b9f6..0dfd43c5b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -50,7 +50,7 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction wit
@Output
protected var genotypeStats: File = null
- override val defaultVmem = "4G"
+ override val defaultCoreMemory = 3.0
override val defaultThreads = 3
protected var outputDir: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
index 85919fb55..a10882b81 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
@@ -50,8 +50,7 @@ class VepNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunctio
var mode: String = config("mode", default = "explode")
var doNotRemove: Boolean = config("donotremove", default = false)
- memoryLimit = Some(1.0)
- override val defaultVmem = "4G"
+ override val defaultCoreMemory = 1.0
override def commandLine = super.commandLine +
required("-I", inputVCF) +
--
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