diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala index 2b87af30dd320372e784b0bacd2556e1ba0e9b86..ef97ed813055cd483b08ce41f476eb61a70914f4 100644 --- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala +++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala @@ -58,6 +58,8 @@ class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction]) var log_to_file: File = _ + override def defaultCoreMemory = 4.0 + override def beforeGraph() = { super.beforeGraph() if (reference == null) reference = referenceFasta() diff --git a/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala b/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala index 37009ba2378398e441270603b53809bd3f01ef44..1ea41dd50ba72e833f166a0b51135f499d86316f 100644 --- a/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala +++ b/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala @@ -29,6 +29,8 @@ class ValidateFastq(val root: Configurable) extends ToolCommandFunction { @Input(doc = "Input R1 fastq file", required = false) var r2Fastq: Option[File] = None + override def defaultCoreMemory = 4.0 + override def cmdLine = super.cmdLine + required("-i", r1Fastq) + optional("-j", r2Fastq)