diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala index 300cd4cdb0d240f19c709ac53e35b180e8675504..11fffa46f9db675245fb5ff718b2452fd6b1d595 100644 --- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala +++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala @@ -28,7 +28,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable { var residentFactor: Double = config("resident_factor", default = 1.2) private var _coreMemory: Double = 2.0 - def coreMemeory = _coreMemory + def coreMemory = _coreMemory var retry = 0 @@ -89,7 +89,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable { commands.foreach(_.setResources()) nCoresRequest = Some(commands.map(_.threads).sum) - _coreMemory = commands.map(cmd => cmd.coreMemeory * (cmd.threads.toDouble / threads.toDouble)).sum + _coreMemory = commands.map(cmd => cmd.coreMemory * (cmd.threads.toDouble / threads.toDouble)).sum memoryLimit = Some(_coreMemory * threads) residentLimit = Some((_coreMemory + (0.5 * retry)) * residentFactor) vmem = Some((_coreMemory * (vmemFactor + (0.5 * retry))) + "G") diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala index eaef86a39e2d02e22b49cb2a0a9a12073b841934..b70865176acc39ad3946c6acbf13dda83599b53c 100644 --- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala +++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala @@ -29,6 +29,8 @@ class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction { @Input(doc = "Input wig file") var inputWigFile: File = _ + override def defaultCoreMemory = 3.0 + @Input(doc = "Input chrom sizes file", required = true) var inputChromSizesFile: File = _ diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala index 5df2a3a7b47f5771dcdbd033ef2c273ba70ed89f..1e145929642f9c0c29e1cd8f07b9eb0a8fcf3da6 100644 --- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala +++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala @@ -27,7 +27,7 @@ class SamtoolsSort(val root: Configurable) extends Samtools { } def cmdLine = required(executable) + required("sort") + - optional("-m", (coreMemeory + "G")) + + optional("-m", (coreMemory + "G")) + optional("-@", threads) + optional("-O", outputFormat) + required("-T", prefix) +