Commit 9d0b9d7e authored by Peter van 't Hof's avatar Peter van 't Hof

Fix format

parent b632a8b4
package nl.lumc.sasc.biopet.core package nl.lumc.sasc.biopet.core
import java.io.{File, PrintWriter} import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.utils.summary.Summary import nl.lumc.sasc.biopet.utils.summary.Summary
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Question, ToolCommand} import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Question, ToolCommand }
import scala.io.Source import scala.io.Source
...@@ -58,7 +57,7 @@ trait TemplateTool extends ToolCommand { ...@@ -58,7 +57,7 @@ trait TemplateTool extends ToolCommand {
case Some(f) => f case Some(f) => f
case _ => sys.env.get("BIOPET_SCRIPT_TEMPLATE") match { case _ => sys.env.get("BIOPET_SCRIPT_TEMPLATE") match {
case Some(file) => new File(file) case Some(file) => new File(file)
case _ => throw new IllegalArgumentException("No template found on argument or 'BIOPET_SCRIPT_TEMPLATE'") case _ => throw new IllegalArgumentException("No template found on argument or 'BIOPET_SCRIPT_TEMPLATE'")
} }
} }
......
...@@ -46,6 +46,7 @@ object BiopetExecutableMain extends BiopetExecutable { ...@@ -46,6 +46,7 @@ object BiopetExecutableMain extends BiopetExecutable {
def templates: List[MainCommand] = List( def templates: List[MainCommand] = List(
nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping, nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping,
nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva,
nl.lumc.sasc.biopet.pipelines.gentrap.template.Gentrap
) )
} }
...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.template ...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.template
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.TemplateTool import nl.lumc.sasc.biopet.core.TemplateTool
import nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.{ExpMeasures, StrandProtocol} import nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.{ ExpMeasures, StrandProtocol }
import nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping import nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping
import nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva import nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva
import nl.lumc.sasc.biopet.utils._ import nl.lumc.sasc.biopet.utils._
...@@ -43,10 +43,10 @@ object Gentrap extends TemplateTool { ...@@ -43,10 +43,10 @@ object Gentrap extends TemplateTool {
"strand_protocol" -> strandProtocol, "strand_protocol" -> strandProtocol,
"annotation_refflat" -> annotationRefFlat "annotation_refflat" -> annotationRefFlat
) ++ (if (Question.boolean("Call variants")) { ) ++ (if (Question.boolean("Call variants")) {
val variantCallers = Question.list("Variantcallers", posibleValues = Shiva.possibleVariantcallers, val variantCallers = Question.list("Variantcallers", posibleValues = Shiva.possibleVariantcallers,
default = Some(List("varscan_cns_singlesample"))) default = Some(List("varscan_cns_singlesample")))
Map("call_variants" -> true, "variantcallers" -> variantCallers) Map("call_variants" -> true, "variantcallers" -> variantCallers)
} else Map("call_variants" -> false)) } else Map("call_variants" -> false))
} }
} }
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