diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala index c235866389194c2305abcda4e2d04bdef4de04b8..0a4227fc8ce46a3563b53f016099fc64c1dd93ad 100644 --- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala +++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala @@ -64,7 +64,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript } /** Variantcallers requested by the config */ - protected val configCallers: Set[String] = config("sv_callers") + protected val configCallers: Set[String] = config("sv_callers", default = Set("breakdancer", "clever", "delly")) /** This will add jobs for this pipeline */ def biopetScript(): Unit = { @@ -148,7 +148,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript /** Files for the summary */ def summaryFiles: Map[String, File] = { - val callers: Set[String] = config("sv_callers") + val callers: Set[String] = configCallers //callersList.filter(x => callers.contains(x.name)).map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile) Map() }