Commit 3c8c6fa3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix config error

parent 2d4ea4b7
...@@ -64,7 +64,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript ...@@ -64,7 +64,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
} }
/** Variantcallers requested by the config */ /** 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 */ /** This will add jobs for this pipeline */
def biopetScript(): Unit = { def biopetScript(): Unit = {
...@@ -148,7 +148,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript ...@@ -148,7 +148,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
/** Files for the summary */ /** Files for the summary */
def summaryFiles: Map[String, File] = { 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) //callersList.filter(x => callers.contains(x.name)).map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
Map() Map()
} }
......
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