Update to Queue/GATK 3.2

.gitignore

@@ -4,4 +4,6 @@
 /pipeline-template/nbactions.xml
 /gatk-variantcalling/nbactions.xml
 /gatk-variantcalling/dependency-reduced-pom.xml
-/bam-metrics/nbactions.xml
\ No newline at end of file
+/bam-metrics/nbactions.xml
+dependency-reduced-pom.xml
+nbactions.xml

bam-metrics/pom.xml

@@ -55,7 +55,7 @@
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>queue-package</artifactId>
-            <version>3.1</version>
+            <version>3.2</version>
         </dependency>
     </dependencies>
     <build>

bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
-import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.gatk.queue.QScript
 import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
 import java.io.File
 import nl.lumc.sasc.biopet.core.apps.{BedToInterval, BiopetFlagstat}

bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 
 class CoverageStats(val root:Configurable) extends PythonCommandLineFunction {

biopet-framework/pom.xml

@@ -52,7 +52,7 @@
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>queue-package</artifactId>
-            <version>3.1</version>
+            <version>3.2</version>
         </dependency>
     </dependencies>
     <build>

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

 package nl.lumc.sasc.biopet.core
 
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import scala.sys.process._
 import nl.lumc.sasc.biopet.core.config._
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.queue.QException
-import org.broadinstitute.sting.queue.function.CommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.queue.QException
+import org.broadinstitute.gatk.queue.function.CommandLineFunction
+import org.broadinstitute.gatk.utils.commandline._
 import scala.sys.process._
 import scala.util.matching.Regex
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

 package nl.lumc.sasc.biopet.core
 
-import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
+import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
 
 abstract class BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
   executeble = "java"

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala

@@ -27,21 +27,21 @@
 package nl.lumc.sasc.biopet.core
 
 import java.io.File
-import org.broadinstitute.sting.commandline._
-import org.broadinstitute.sting.queue.util._
-import org.broadinstitute.sting.queue.QCommandPlugin
-import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.QScriptManager
-import org.broadinstitute.sting.queue.engine.{QStatusMessenger, QGraphSettings, QGraph}
+import org.broadinstitute.gatk.utils.commandline._
+import org.broadinstitute.gatk.queue.util._
+import org.broadinstitute.gatk.queue.QCommandPlugin
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.QScriptManager
+import org.broadinstitute.gatk.queue.engine.{QStatusMessenger, QGraphSettings, QGraph}
 import collection.JavaConversions._
-import org.broadinstitute.sting.utils.classloader.PluginManager
-import org.broadinstitute.sting.utils.exceptions.UserException
-import org.broadinstitute.sting.utils.io.IOUtils
-import org.broadinstitute.sting.utils.help.ApplicationDetails
+import org.broadinstitute.gatk.utils.classloader.PluginManager
+import org.broadinstitute.gatk.utils.exceptions.UserException
+import org.broadinstitute.gatk.utils.io.IOUtils
+import org.broadinstitute.gatk.utils.help.ApplicationDetails
 import java.io.FileOutputStream
 import java.net.URL
 import java.util.{ResourceBundle, Arrays}
-import org.broadinstitute.sting.utils.text.TextFormattingUtils
+import org.broadinstitute.gatk.utils.text.TextFormattingUtils
 import org.apache.commons.io.FilenameUtils
 
 /**

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -3,9 +3,9 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 import java.io.PrintWriter
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
-import org.broadinstitute.sting.queue.QSettings
-import org.broadinstitute.sting.queue.function.QFunction
+import org.broadinstitute.gatk.utils.commandline._
+import org.broadinstitute.gatk.queue.QSettings
+import org.broadinstitute.gatk.queue.function.QFunction
 
 trait BiopetQScript extends Configurable {
   @Argument(doc="Config Json file",shortName="config", required=false)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.FileOutputStream
 //import org.broadinstitute.sting.queue.QCommandLine
-import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.gatk.queue.util.Logging
 
 trait PipelineCommand extends Logging {
 //  val src = ""

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BedToInterval.scala

 package nl.lumc.sasc.biopet.core.apps
 
+import htsjdk.samtools.SAMFileReader
+import htsjdk.samtools.SAMSequenceRecord
 import java.io.File
-import net.sf.samtools.SAMSequenceRecord
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 import java.io.PrintWriter
-import net.sf.samtools.SAMFileReader
 import scala.io.Source
 
 class BedToInterval(val root:Configurable) extends BiopetJavaCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala

 package nl.lumc.sasc.biopet.core.apps
 
+import htsjdk.samtools.SAMFileReader
+import htsjdk.samtools.SAMRecord
 import java.io.{BufferedInputStream, File, FileInputStream, PrintWriter}
-import net.sf.samtools.SAMFileReader
-import net.sf.samtools.SAMRecord
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import scala.io.Source
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Input, Output}
-import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.queue.util.Logging
 import scala.collection.JavaConversions._
 import scala.collection.mutable.Map
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/FastqSplitter.scala

@@ -5,7 +5,7 @@ import java.util.zip.GZIPInputStream
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import scala.io.Source
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
 class FastqSplitter(val root:Configurable) extends BiopetJavaCommandLineFunction {
   javaMainClass = getClass.getName

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core.config
 import nl.lumc.sasc.biopet.core._
 import scala.util.parsing.json._
 import java.io.File
-import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.gatk.queue.util.Logging
 
 class Config(var map: Map[String,Any]) extends Logging {
   logger.debug("Init phase of config")

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

 package nl.lumc.sasc.biopet.core.config
 
 import java.io.File
-import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.gatk.queue.util.Logging
 
 trait Configurable extends Logging {
   val root: Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 
 class Cat(val root:Configurable) extends BiopetCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala

@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.function
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.queue.function.InProcessFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 import scala.sys.process._
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.function
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 //import org.broadinstitute.sting.queue.function.CommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 
 class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
 
 import java.io.FileOutputStream
 import nl.lumc.sasc.biopet.core._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 import scala.collection.JavaConversions._
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 
 class Sha1sum(val root:Configurable) extends BiopetCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline._
 import java.io.File
 
 class Zcat(val root:Configurable) extends BiopetCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala

 package nl.lumc.sasc.biopet.function.bedtools
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Input, Output, Argument}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 
 class BedtoolsCoverage(val root:Configurable) extends Bedtools {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala

 package nl.lumc.sasc.biopet.function.bedtools
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Input, Output, Argument}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 
 class BedtoolsIntersect(val root:Configurable) extends Bedtools {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Argument, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 class CalculateHsMetrics(val root:Configurable) extends Picard {
   javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics"

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectGcBiasMetrics.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Argument, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 class CollectGcBiasMetrics(val root:Configurable) extends Picard {
   javaMainClass = "net.sf.picard.analysis.CollectGcBiasMetrics"

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectInsertSizeMetrics.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Argument, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 class CollectInsertSizeMetrics(val root:Configurable) extends Picard {
   javaMainClass = "net.sf.picard.analysis.CollectInsertSizeMetrics"

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Argument, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 class MarkDuplicates(val root:Configurable) extends Picard {
   javaMainClass = "net.sf.picard.sam.MarkDuplicates"

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala

 package nl.lumc.sasc.biopet.function.picard
 
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 trait Picard extends BiopetJavaCommandLineFunction {
   @Argument(doc="VERBOSITY", required = false)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala

 package nl.lumc.sasc.biopet.function.samtools
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.sting.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 import java.io.File
 
 class SamtoolsFlagstat(val root:Configurable) extends Samtools {

flexiprep/pom.xml

@@ -50,7 +50,7 @@
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>queue-package</artifactId>
-            <version>3.1</version>
+            <version>3.2</version>
         </dependency>
     </dependencies>
     <build>

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.fastq
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 import scala.io.Source._
 import scala.sys.process._

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.fastq
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 import scala.sys.process._
 

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.fastq
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 import scala.io.Source._
 import scala.sys.process._

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -4,12 +4,12 @@ import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function._
 import nl.lumc.sasc.biopet.function.fastq._
-import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.extensions.gatk._
-import org.broadinstitute.sting.queue.extensions.picard._
-import org.broadinstitute.sting.queue.function._
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.extensions.gatk._
+import org.broadinstitute.gatk.queue.extensions.picard._
+import org.broadinstitute.gatk.queue.function._
 import scala.util.parsing.json._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
 
 class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala

@@ -4,7 +4,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 
 class FastqSync(val root:Configurable) extends PythonCommandLineFunction {

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 
 class FastqcToContams(val root:Configurable) extends PythonCommandLineFunction {

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 
 class FastqcToQualtype(val root:Configurable) extends PythonCommandLineFunction {

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 
 class Seqstat(val root:Configurable) extends PythonCommandLineFunction {

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 
 class Summarize(val root:Configurable) extends PythonCommandLineFunction {

gatk-genotyping/pom.xml

@@ -50,7 +50,7 @@
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>queue-package</artifactId>
-            <version>3.1</version>
+            <version>3.2</version>
         </dependency>
     </dependencies>
     <build>

gatk-genotyping/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

@@ -3,10 +3,10 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function._
-import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.extensions.gatk.{CommandLineGATK, GenotypeGVCFs, SelectVariants}
-import org.broadinstitute.sting.queue.function._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.extensions.gatk.{CommandLineGATK, GenotypeGVCFs, SelectVariants}
+import org.broadinstitute.gatk.queue.function._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 
 class GatkGenotyping(val root:Configurable) extends QScript with BiopetQScript {
   def this() = this(null)

gatk-variantcalling/pom.xml

@@ -50,7 +50,7 @@
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>queue-package</artifactId>
-            <version>3.1</version>
+            <version>3.2</version>
         </dependency>
     </dependencies>
     <build>

gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function._
-import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.extensions.gatk.{BaseRecalibrator, CommandLineGATK, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, GenotypeGVCFs, AnalyzeCovariates}
-import org.broadinstitute.sting.queue.function._
-import org.broadinstitute.sting.commandline._
-import org.broadinstitute.sting.utils.variant.GATKVCFIndexType
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.extensions.gatk.{BaseRecalibrator, CommandLineGATK, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, GenotypeGVCFs, AnalyzeCovariates}
+import org.broadinstitute.gatk.queue.function._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
+import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
 
 class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScript {
   def this() = this(null)
@@ -126,7 +126,7 @@ class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScri
       
       // GVCF options
       if (gvcfMode) {
-        this.emitRefConfidence = org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.ReferenceConfidenceMode.GVCF
+        this.emitRefConfidence = org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceMode.GVCF
         this.variant_index_type = GATKVCFIndexType.LINEAR
         this.variant_index_parameter = 128000
       }

gatk/pom.xml

@@ -60,7 +60,7 @@
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>queue-package</artifactId>
-            <version>3.1</version>
+            <version>3.2</version>
         </dependency>
     </dependencies>
     <build>

gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala

@@ -2,18 +2,19 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.function._
 import nl.lumc.sasc.biopet.function.aligners._
+import java.io.File
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.pipelines.mapping._
 import nl.lumc.sasc.biopet.function.picard.MarkDuplicates
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.flexiprep._
-import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.extensions.gatk._
-import org.broadinstitute.sting.queue.extensions.picard._
-import org.broadinstitute.sting.queue.function._
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.extensions.gatk._
+import org.broadinstitute.gatk.queue.extensions.picard._
+import org.broadinstitute.gatk.queue.function._
+import org.broadinstitute.gatk.utils.commandline.{Argument}
 import scala.util.parsing.json._
-import org.broadinstitute.sting.utils.variant.GATKVCFIndexType
 
 class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
   def this() = this(null)
@@ -150,7 +151,7 @@ class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
       this.out = swapExt(dir,inputBam,".bam",".split.bam")
       this.read_filter :+= "ReassignMappingQuality"
       
-      this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.ALLOW_N_CIGAR_READS
+      this.U = org.broadinstitute.gatk.engine.arguments.ValidationExclusion.TYPE.ALLOW_N_CIGAR_READS
     }
     add(splitNCigarReads)
     
@@ -167,8 +168,8 @@ class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
       this.memoryLimit = this.nct * 2
       
       // GVCF options
-      this.emitRefConfidence = org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.ReferenceConfidenceMode.GVCF
-      this.variant_index_type = GATKVCFIndexType.LINEAR
+      this.emitRefConfidence =  org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceMode.GVCF
+      this.variant_index_type = org.broadinstitute.gatk.utils.variant.GATKVCFIndexType.LINEAR
       this.variant_index_parameter = 128000
       
       val inputType:String = config("inputtype", "dna")
@@ -226,10 +227,10 @@ class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
   def getVariantRecalibrator(mode_arg:String) : VariantRecalibrator = {
     val variantRecalibrator = new VariantRecalibrator() with gatkArguments {
       if (mode_arg == "indel") {
-        this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
+        this.mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
         if (configContains("mills", "variantrecalibrator")) this.resource :+= new TaggedFile(config("mills", "", "variantrecalibrator").getString, "known=false,training=true,truth=true,prior=12.0")
       } else { // SNP
-        this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
+        this.mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
         if (configContains("hapmap", "variantrecalibrator")) this.resource +:= new TaggedFile(config("hapmap", "", "variantrecalibrator").getString, "known=false,training=true,truth=true,prior=15.0")
         if (configContains("omni", "variantrecalibrator")) this.resource +:= new TaggedFile(config("omni", "", "variantrecalibrator").getString, "known=false,training=true,truth=true,prior=12.0")
         if (configContains("1000G", "variantrecalibrator")) this.resource +:= new TaggedFile(config("1000G", "", "variantrecalibrator").getString, "known=false,training=true,truth=false,prior=10.0")
@@ -247,10 +248,10 @@ class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
   def getApplyRecalibration(mode_arg:String) : ApplyRecalibration = {
     val applyRecalibration = new ApplyRecalibration() with gatkArguments {
       if (mode_arg == "indel") {
-        this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
+        this.mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
         this.ts_filter_level = config("ts_filter_level", 99.0, "applyrecalibration")
       } else { // SNP
-        this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
+        this.mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
         this.ts_filter_level = config("ts_filter_level", 99.5, "applyrecalibration")
       }
       this.nt = 3

mapping/pom.xml

@@ -60,7 +60,7 @@
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>queue-package</artifactId>
-            <version>3.1</version>
+            <version>3.2</version>
         </dependency>
     </dependencies>
     <build>

mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.aligners
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 import scala.sys.process._
 

mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.aligners
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.sting.commandline._
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
 import java.io.File
 import scala.sys.process._
 

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -10,14 +10,14 @@ import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.function.picard.MarkDuplicates
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.flexiprep._
-import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.extensions.gatk._
-import org.broadinstitute.sting.queue.extensions.picard.MergeSamFiles