Commit 0a33b3d3 authored by Peter van 't Hof's avatar Peter van 't Hof

Update to Queue/GATK 3.2

parent 719894d1
......@@ -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
......@@ -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>
......
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}
......
......@@ -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 {
......
......@@ -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>
......
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._
......
......@@ -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
......
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"
......
......@@ -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
/**
......
......@@ -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)
......
......@@ -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 = ""
......
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 {
......
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
......
......@@ -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
......
......@@ -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")
......
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
......
......@@ -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 {
......
......@@ -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._
......
......@@ -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 {
......
......@@ -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._
......
......@@ -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 {
......
......@@ -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 {
......
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 {
......
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 {
......
......@@ -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"
......
......@@ -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"
......
......@@ -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"
......
......@@ -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"
......
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)
......
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 {
......
......@@ -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>
......
......@@ -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._
......
......@@ -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._
......
......@@ -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._
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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>
......
......@@ -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)
......
......@@ -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>
......
......@@ -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
}
......
......@@ -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>
......
......@@ -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
......
......@@ -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>
......
......@@ -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._
......
......@@ -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._
......
......@@ -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
import org.broadinstitute.sting.queue.extensions.picard.SortSam
import org.broadinstitute.sting.queue.extensions.picard.AddOrReplaceReadGroups
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.MergeSamFiles
import org.broadinstitute.gatk.queue.extensions.picard.SortSam
import org.broadinstitute.gatk.queue.extensions.picard.AddOrReplaceReadGroups
import org.broadinstitute.gatk.queue.function._
import scala.util.parsing.json._
import org.broadinstitute.sting.utils.variant._
import org.broadinstitute.gatk.utils.variant._
import scala.math._
class Mapping(val root:Configurable) extends QScript with BiopetQScript {
......
......@@ -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>
......
......@@ -3,9 +3,9 @@ package nl.lumc.sasc.biopet.pipelines.pipelinetemplate
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.function._
import org.broadinstitute.sting.commandline._
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function._
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
class PipelineTemplate(val root:Configurable) extends QScript with BiopetQScript {
def this() = this(null)
......
......@@ -14,5 +14,6 @@