From 1fb2569e031da6f82b0085a0daab92c5b758cbd6 Mon Sep 17 00:00:00 2001
From: Sander van der Zeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Mon, 6 Jul 2015 16:01:15 +0200
Subject: [PATCH] Added defaults to gsnap for sam format
---
.../nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 98b3aa0fc..fcc89a029 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -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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