Commit 705d9cd6 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Style fixes and config for samtofastq

parent 4cb2adf1
......@@ -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)
......
......@@ -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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