Commit ca40d875 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

move varscan wrapper to extensions

parent bb46c239
package nl.lumc.sasc.biopet.extensions.varscan
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by sajvanderzeeuw on 19-1-16.
*/
class FixMpileup(val root: Configurable) extends PythonCommandLineFunction {
setPythonScript("fix_mpileup.py", "/nl/lumc/sasc/biopet/extensions/varscan/")
def cmdLine = getPythonCommand
}
...@@ -2,12 +2,10 @@ package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers ...@@ -2,12 +2,10 @@ package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import java.io.PrintWriter import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.{ Ln, Tabix, Bgzip }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.extensions.varscan.VarscanMpileup2cns import nl.lumc.sasc.biopet.extensions.varscan.{ FixMpileup, VarscanMpileup2cns }
import nl.lumc.sasc.biopet.extensions.{Bgzip, Tabix}
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
/** /**
...@@ -44,17 +42,10 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller { ...@@ -44,17 +42,10 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
writer.println(sample) writer.println(sample)
writer.close() writer.close()
val fixMpileup = new PythonCommandLineFunction {
setPythonScript("fix_mpileup.py", "/nl/lumc/sasc/biopet/pipelines/shiva/scripts/")
override val root: Configurable = this.root
override def configName = "fix_mpileup"
def cmdLine = getPythonCommand
}
val varscan = new VarscanMpileup2cns(this) val varscan = new VarscanMpileup2cns(this)
varscan.vcfSampleList = Some(sampleFile) varscan.vcfSampleList = Some(sampleFile)
add(mpileup | fixMpileup | varscan | new Bgzip(this) > sampleVcf) add(mpileup | new FixMpileup(this) | varscan | new Bgzip(this) > sampleVcf)
add(Tabix(this, sampleVcf)) add(Tabix(this, sampleVcf))
sampleVcf sampleVcf
......
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