diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala index 17894a8154915e4dd7e0ec995d638b2e8d68182d..6da7c3ed11c0c589adc3863be9e15cb671056b55 100644 --- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala +++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala @@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version} /** General Sambamba extension */ abstract class Sambamba extends BiopetCommandLineFunction with Version { - override def defaultCoreMemory = 2.0 + override def defaultCoreMemory = 4.0 override def defaultThreads = 2 override def subPath = "sambamba" :: super.subPath diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala index d25d04f8411545bb05cf099dc1cd177b18590009..aabbedb8629246b1695387125ae508d66bd12252 100644 --- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala +++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala @@ -73,14 +73,13 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam def biopetScript(): Unit = { val fastqFiles: List[File] = bamFile.map { bamfile => -// // sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam> -// val samFilterUnmapped = new SambambaView(this) -// samFilterUnmapped.input = bamfile -// samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment) and [XH] == null") -// samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam") -// samFilterUnmapped.isIntermediate = false -// add(samFilterUnmapped) - + // // sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam> + // val samFilterUnmapped = new SambambaView(this) + // samFilterUnmapped.input = bamfile + // samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment) and [XH] == null") + // samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam") + // samFilterUnmapped.isIntermediate = false + // add(samFilterUnmapped) val samtoolsViewSelectUnmapped = new SamtoolsView(this) samtoolsViewSelectUnmapped.input = bamfile