From b4b21a186c182ae66af794cf264f0ddcfb3d54b4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 Sep 2016 12:06:42 +0200
Subject: [PATCH] Fix summary
---
.../nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
index 06f4a02b3..0f0a04d8d 100644
--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
@@ -45,10 +45,12 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
krakenReportJSON.skipNames = config("skipNames", default = false)
add(krakenReportJSON)
addSummarizable(krakenReportJSON, "centrifugereport")
+
+ addSummaryJobs()
}
/** Location of summary file */
- def summaryFile = new File(outputDir, sampleId.getOrElse("sampleName_unknown") + ".kraken.summary.json")
+ def summaryFile = new File(outputDir, sampleId.getOrElse("sampleName_unknown") + ".centrifuge.summary.json")
/** Pipeline settings shown in the summary file */
def summarySettings: Map[String, Any] = Map()
--
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