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Commit ca53b210 authored by Peter van 't Hof's avatar Peter van 't Hof
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Reduce threads for varscan

parent 79b42eea
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
View file @ ca53b210
...@@ -60,7 +60,9 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller { ...@@ -60,7 +60,9 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
val varscan = new VarscanMpileup2cns(this) val varscan = new VarscanMpileup2cns(this)
varscan.vcfSampleList = Some(sampleFile) 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)) add(Tabix(this, sampleVcf))
sampleVcf sampleVcf
......
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