From 2f92eb6d441247e31731246f3cc48199c7d0c829 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 29 Oct 2015 16:42:47 +0100
Subject: [PATCH] Fixed summary file name
---
.../nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala | 4 ++--
.../lumc/sasc/biopet/extensions/sambamba/Sambamba.scala | 2 +-
.../sasc/biopet/extensions/tools/KrakenReportToJson.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala | 8 ++++----
.../nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala | 4 ++--
6 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
index 6e0905e9f..86df5c415 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
@@ -18,9 +18,9 @@ package nl.lumc.sasc.biopet.extensions.kraken
import java.io.File
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for Kraken */
class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Version {
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
index 6da7c3ed1..b12ff9584 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.extensions.sambamba
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
/** General Sambamba extension */
abstract class Sambamba extends BiopetCommandLineFunction with Version {
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 df97f7bb1..475d0b0b2 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
@@ -9,7 +9,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFunction
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, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* KrakenReportToJson function class for usage in Biopet pipelines
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
index 3fa672cfa..ee59a22aa 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
@@ -19,7 +19,7 @@ package nl.lumc.sasc.biopet.tools
* Created by wyleung on 25-9-15.
*/
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.ConfigUtils._
import nl.lumc.sasc.biopet.utils.ToolCommand
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 aabbedb86..53dcb1df3 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
@@ -16,11 +16,11 @@
package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{PipelineCommand, SampleLibraryTag}
-import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
+import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
-import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, KrakenReportToJson}
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, KrakenReportToJson }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
@@ -158,7 +158,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
}
/** Location of summary file */
- def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".gears.summary.json")
+ def summaryFile = new File(outputDir, sampleId.getOrElse("sampleName_unknown") + ".gears.summary.json")
/** Pipeline settings shown in the summary file */
def summarySettings: Map[String, Any] = Map.empty
diff --git a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
index 909163554..64add1908 100644
--- a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
+++ b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
+import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
-import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, KrakenReportToJson}
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, KrakenReportToJson }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
--
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