From 72a96f7e5b377d20853d1d6b31f4aa9066b595c2 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 30 Oct 2015 14:37:03 +0100
Subject: [PATCH] Adding Gears to summary output of Mapping
---
.../nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
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 eb52e5ab9..c56a48b2d 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
@@ -19,18 +19,17 @@ import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.pipelines.gears.Gears
-import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
+import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions.{ Gsnap, Tophat, _ }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
+import nl.lumc.sasc.biopet.pipelines.gears.Gears
import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
-import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import scala.math._
@@ -266,6 +265,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
gears.init()
gears.biopetScript()
addAll(gears.functions)
+ addSummaryQScript(gears)
}
if (config("generate_wig", default = false).asBoolean)
--
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