From 189a25d4ec6c86860e177ea79fe7df0278fbcd9c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 12 Jan 2016 12:58:27 +0100
Subject: [PATCH] Added html report to pipeline
---
.../nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index fbb095945..62d004d63 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.FullVersion
import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
@@ -53,6 +54,13 @@ class Gentrap(val root: Configurable) extends QScript
// alternative constructor for initialization with empty configuration
def this() = this(null)
+ override def reportClass: Option[ReportBuilderExtension] = {
+ val report = new GentrapReport(this)
+ report.outputDir = new File(outputDir, "report")
+ report.summaryFile = summaryFile
+ Some(report)
+ }
+
/** Split aligner to use */
var aligner: String = config("aligner", default = "gsnap")
--
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