Commit 3f7a6044 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed md5sums

parent 32692078
......@@ -67,15 +67,16 @@ trait ShivaVariantcallingTrait extends SummaryQScript
/** Variantcallers requested by the config */
protected val configCallers: Set[String] = config("variantcallers")
protected val callers: List[Variantcaller] = {
(for (name <- configCallers) yield {
if (!callersList.exists(_.name == name))
Logging.addError(s"variantcaller '$name' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
callersList.find(_.name == name)
}).flatten.toList.sortBy(_.prio)
}
/** This will add jobs for this pipeline */
def biopetScript(): Unit = {
for (cal <- configCallers) {
if (!callersList.exists(_.name == cal))
Logging.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
}
val callers = callersList.filter(x => configCallers.contains(x.name)).sortBy(_.prio)
require(inputBams.nonEmpty, "No input bams found")
require(callers.nonEmpty, "must select at least 1 variantcaller, choices are: " + callersList.map(_.name).mkString(", "))
......@@ -168,7 +169,6 @@ trait ShivaVariantcallingTrait extends SummaryQScript
/** Files for the summary */
def summaryFiles: Map[String, File] = {
val callers: Set[String] = config("variantcallers")
callersList.filter(x => callers.contains(x.name)).map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
callers.map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
}
}
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