From e133158f00abce5fd6092b3eae57c94b383a8361 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 25 Dec 2015 14:34:08 +0100
Subject: [PATCH] Changes name
---
.../nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
index a57d62ebb..8ef51a20f 100644
--- a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
+++ b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
@@ -12,13 +12,13 @@
<%@ var outputDir: File %>
<%
- val bla = if (sampleId.isEmpty && libId.isEmpty) {
+ val summaries = if (sampleId.isEmpty && libId.isEmpty) {
summary.getSampleValues("gearskraken", "stats", "krakenreport").map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
} else summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
val tempFile = File.createTempFile("krona.", ".xml")
tempFile.deleteOnExit()
- GearsKraken.convertKrakenSummariesToKronaXml(bla, tempFile)
+ GearsKraken.convertKrakenSummariesToKronaXml(summaries, tempFile)
val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/krona.ssp",
args ++ Map("kronaXml" -> tempFile))
--
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