diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala index 2be78c7226036ef90021d8bfc144a225c0460ab5..fb900410363933159cbf0da593ac9a33013f8026 100644 --- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala +++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala @@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.config._ import nl.lumc.sasc.biopet.core.summary.SummaryQScript import nl.lumc.sasc.biopet.extensions.Ln import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak -import nl.lumc.sasc.biopet.extensions.picard.{BuildBamIndex, MergeSamFiles} +import nl.lumc.sasc.biopet.extensions.picard.{ BuildBamIndex, MergeSamFiles } import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig import nl.lumc.sasc.biopet.pipelines.mapping.Mapping @@ -46,7 +46,14 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with ), "samtoolsview" -> Map("q" -> 10) ) - + + override def fixedValues = Map( + "samtoolsview" -> Map( + "h" -> true, + "b" -> true + ) + ) + def summaryFile = new File(outputDir, "Carp.summary.json") //TODO: Add summary @@ -122,8 +129,6 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with val samtoolsView = new SamtoolsView(qscript) samtoolsView.input = bamFile samtoolsView.output = bamFileFilter - samtoolsView.b = true - samtoolsView.h = true add(samtoolsView) val buildBamIndex = new BuildBamIndex(qscript)