From 705d9cd62eb280ab9d0c619c707c669740f3a46b Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Thu, 29 Oct 2015 13:27:48 +0100
Subject: [PATCH] Style fixes and config for samtofastq
---
.../lumc/sasc/biopet/extensions/sambamba/Sambamba.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala | 8 ++++++--
2 files changed, 8 insertions(+), 4 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 12c6a5024..17894a815 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
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.extensions.sambamba
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
/** General Sambamba extension */
abstract class Sambamba extends BiopetCommandLineFunction with Version {
@@ -24,7 +24,7 @@ abstract class Sambamba extends BiopetCommandLineFunction with Version {
override def subPath = "sambamba" :: super.subPath
- executable = config("exe", default = "sambamba", submodule = "sambamba")
+ executable = config("exe", default = "sambamba", submodule = "sambamba", freeVar = false)
def versionCommand = executable
def versionRegex = """sambamba v(.*)""".r
override def versionExitcode = List(0, 1)
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 63e032815..895ad38ad 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
@@ -63,9 +63,14 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
gears.summaryFile = summaryFile
Some(gears)
}
+
+ override def defaults = Map(
+ "samtofastq" -> Map(
+ "validationstringency" -> "LENIENT"
+ )
+ )
/** Method to add jobs */
def biopetScript(): Unit = {
-
val fastqFiles: List[File] = bamFile.map { bamfile =>
// sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
@@ -79,7 +84,6 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
// start bam to fastq (only on unaligned reads) also extract the matesam
val samToFastq = new SamToFastq(this)
samToFastq.input = samFilterUnmapped.output
- samToFastq.stringency = Some("LENIENT")
samToFastq.fastqR1 = new File(outputDir, s"$outputName.unmapped.R1.fq.gz")
samToFastq.fastqR2 = new File(outputDir, s"$outputName.unmapped.R2.fq.gz")
samToFastq.fastqUnpaired = new File(outputDir, s"$outputName.unmapped.singleton.fq.gz")
--
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