Commit 1fb2569e authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

Added defaults to gsnap for sam format

parent fa3d5fbc
......@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import java.util.Date
import java.io.File
import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import nl.lumc.sasc.biopet.utils.ConfigUtils
import scala.math._
......@@ -98,6 +99,14 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** location of summary file */
def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".summary.json")
override def defaults = ConfigUtils.mergeMaps(
Map(
"gsnap" -> Map(
"batch" -> 4,
"format" -> "sam"
)
), super.defaults)
/** File to add to the summary */
def summaryFiles: Map[String, File] = Map("output_bamfile" -> finalBamFile, "input_R1" -> input_R1,
"reference" -> referenceFasta()) ++
......
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