Commit 755b864d authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

More style fixes

parent 8a15fe3c
......@@ -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
......
......@@ -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
......
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