Reduce threads for varscan

ca53b210 · Peter van 't Hof · 79b42eea · ca53b210
Commit ca53b210 authored Aug 15, 2016 by Peter van 't Hof
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
@@ -60,7 +60,9 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
      val varscan = new VarscanMpileup2cns(this)
      varscan.vcfSampleList = Some(sampleFile)

-      add(mpileup | new FixMpileup(this) | varscan | new Bgzip(this) > sampleVcf)
+      val variantcallingJob = mpileup | new FixMpileup(this) | varscan | new Bgzip(this) > sampleVcf
+      variantcallingJob.threadsCorrection = -2
+      add(variantcallingJob)
      add(Tabix(this, sampleVcf))

      sampleVcf