Commit 2f92eb6d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed summary file name

parent 11fe02b4
...@@ -18,9 +18,9 @@ package nl.lumc.sasc.biopet.extensions.kraken ...@@ -18,9 +18,9 @@ package nl.lumc.sasc.biopet.extensions.kraken
import java.io.File 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 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 */ /** Extension for Kraken */
class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Version { class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Version {
......
...@@ -15,7 +15,7 @@ ...@@ -15,7 +15,7 @@
*/ */
package nl.lumc.sasc.biopet.extensions.sambamba 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 */ /** General Sambamba extension */
abstract class Sambamba extends BiopetCommandLineFunction with Version { abstract class Sambamba extends BiopetCommandLineFunction with Version {
......
...@@ -9,7 +9,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFunction ...@@ -9,7 +9,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFunction
import nl.lumc.sasc.biopet.core.summary.Summarizable import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.utils.ConfigUtils import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable 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 * KrakenReportToJson function class for usage in Biopet pipelines
......
...@@ -19,7 +19,7 @@ package nl.lumc.sasc.biopet.tools ...@@ -19,7 +19,7 @@ package nl.lumc.sasc.biopet.tools
* Created by wyleung on 25-9-15. * 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.ConfigUtils._
import nl.lumc.sasc.biopet.utils.ToolCommand import nl.lumc.sasc.biopet.utils.ToolCommand
......
...@@ -16,11 +16,11 @@ ...@@ -16,11 +16,11 @@
package nl.lumc.sasc.biopet.pipelines.gears package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.summary.SummaryQScript import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{PipelineCommand, SampleLibraryTag} import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
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.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView 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 nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
...@@ -158,7 +158,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam ...@@ -158,7 +158,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
} }
/** Location of summary file */ /** 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 */ /** Pipeline settings shown in the summary file */
def summarySettings: Map[String, Any] = Map.empty def summarySettings: Map[String, Any] = Map.empty
......
...@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.pipelines.gears ...@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File import java.io.File
import com.google.common.io.Files 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.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView 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.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
......
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