Commit 20cd7b6d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added input file checking

parent b7743a6e
......@@ -119,5 +119,5 @@ trait BiopetQScript extends Configurable with GatkLogging {
}
object BiopetQScript {
protected case class InputFile(file: File, md5: Option[String] = None)
case class InputFile(file: File, md5: Option[String] = None)
}
......@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
......@@ -55,6 +56,13 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
.getOrElse("noName")
else outputName = bamFile.map(_.getName.stripSuffix(".bam")).getOrElse("noName")
}
if (fastqR1.isDefined) {
fastqR1.foreach(inputFiles :+= InputFile(_))
fastqR2.foreach(inputFiles :+= InputFile(_))
} else {
inputFiles :+= InputFile(bamFile.get)
}
}
override def reportClass = {
......
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