From 755b864dd57cd17569e151680f741c6a0bff3cd1 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Thu, 29 Oct 2015 13:43:06 +0100
Subject: [PATCH] More style fixes
---
.../biopet/extensions/sambamba/Sambamba.scala | 2 +-
.../lumc/sasc/biopet/pipelines/gears/Gears.scala | 15 +++++++--------
2 files changed, 8 insertions(+), 9 deletions(-)
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 17894a815..6da7c3ed1 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 d25d04f84..aabbedb86 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
--
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