From 4350c5b5c384b9d062b8f375c0f73ad79ac30bd8 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@e-sensei.nl>
Date: Tue, 6 Oct 2015 10:35:10 +0200
Subject: [PATCH] Adding files to summary json
---
.../biopet/extensions/tools/KrakenReportToJson.scala | 2 +-
.../nl/lumc/sasc/biopet/pipelines/gears/Gears.scala | 10 +++-------
2 files changed, 4 insertions(+), 8 deletions(-)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
index ff54170ba..d6343a7da 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
@@ -10,7 +10,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
/**
* KrakenReportToJson function class for usage in Biopet pipelines
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index caef8b4de..6278de048 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
-import nl.lumc.sasc.biopet.extensions.tools.{KrakenReportToJson, FastqSync}
+import nl.lumc.sasc.biopet.extensions.tools.{ KrakenReportToJson, FastqSync }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
@@ -120,11 +120,6 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
krakenReportJSON.skipNames = config("skipNames", default = true)
add(krakenReportJSON)
-// val krakenReportJSON = new KrakenReportToJson(qscript)
-// krakenReportJSON.input = krakenReport.output
-// krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json")
-// add(krakenReportJSON)
-
addSummaryJobs()
}
@@ -135,7 +130,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
def summarySettings = Map()
/** Files for the summary */
- def summaryFiles = (if (bamFile.isDefined) Map("input_bam" -> bamFile.get) else Map()) ++
+ def summaryFiles: Map[String, File] = Map.empty ++
+ (if (bamFile.isDefined) Map("input_bam" -> bamFile.get) else Map()) ++
(if (fastqFileR1.isDefined) Map("input_R1" -> fastqFileR1.get) else Map())
}
--
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