Convert analysis_type to abstract value

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

@@ -13,8 +13,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class AnalyzeCovariates(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "AnalyzeCovariates"
-  analysis_type = "AnalyzeCovariates"
+  def analysis_type = "AnalyzeCovariates"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -57,8 +57,7 @@ import org.broadinstitute.gatk.utils.commandline.Input
 import org.broadinstitute.gatk.utils.commandline.Output
 
 class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "ApplyRecalibration"
-  analysis_type = "ApplyRecalibration"
+  def analysis_type = "ApplyRecalibration"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -25,8 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 //TODO: check gathering
 class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with ScatterGatherableFunction */ {
-  analysisName = "BaseRecalibrator"
-  analysis_type = "BaseRecalibrator"
+  def analysis_type = "BaseRecalibrator"
   //TODO: check gathering
   //scatterClass = classOf[ReadScatterFunction]
   //setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

@@ -13,8 +13,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
 
 class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "CombineGVCFs"
-  analysis_type = "CombineGVCFs"
+  def analysis_type = "CombineGVCFs"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

@@ -13,8 +13,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class CombineVariants(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "CombineVariants"
-  analysis_type = "CombineVariants"
+  def analysis_type = "CombineVariants"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CommandLineGATK.scala

@@ -7,13 +7,12 @@ import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
 
 trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with Version {
-  analysisName = "CommandLineGATK"
+  analysisName = analysis_type
   javaMainClass = "org.broadinstitute.gatk.engine.CommandLineGATK"
   jarFile = config("gatk_jar")
 
   /** Name of the tool to run */
-  @Argument(fullName = "analysis_type", shortName = "T", doc = "Name of the tool to run", required = true, exclusiveOf = "", validation = "")
-  var analysis_type: String = _
+  def analysis_type: String
 
   /** Input file containing sequence data (BAM or CRAM) */
   @Input(fullName = "input_file", shortName = "I", doc = "Input file containing sequence data (BAM or CRAM)", required = false, exclusiveOf = "", validation = "")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -43,8 +43,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "GenotypeGVCFs"
-  analysis_type = "GenotypeGVCFs"
+  def analysis_type = "GenotypeGVCFs"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

@@ -5,29 +5,17 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-//  if (config("inputtype", default = "dna").asString == "rna") {
-//    dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
-//    stand_call_conf = config("stand_call_conf", default = 5)
-//    stand_emit_conf = config("stand_emit_conf", default = 0)
-//  } else {
-//    dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
-//    stand_call_conf = config("stand_call_conf", default = 5)
-//    stand_emit_conf = config("stand_emit_conf", default = 0)
-//  }
-//
-
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk._
 import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import nl.lumc.sasc.biopet.utils.VcfUtils
-import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, _}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, _ }
 import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
 
 class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "HaplotypeCaller"
-  analysis_type = "HaplotypeCaller"
+  def analysis_type = "HaplotypeCaller"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -13,8 +13,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class IndelRealigner(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "IndelRealigner"
-  analysis_type = "IndelRealigner"
+  def analysis_type = "IndelRealigner"
   scatterClass = classOf[ReadScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = true }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -13,8 +13,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline._
 
 class PrintReads(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "PrintReads"
-  analysis_type = "PrintReads"
+  def analysis_type = "PrintReads"
   scatterClass = classOf[ReadScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = true }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -13,8 +13,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, _ }
 
 class RealignerTargetCreator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "RealignerTargetCreator"
-  analysis_type = "RealignerTargetCreator"
+  def analysis_type = "RealignerTargetCreator"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala

@@ -30,8 +30,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class SelectVariants(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "SelectVariants"
-  analysis_type = "SelectVariants"
+  def analysis_type = "SelectVariants"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -53,8 +53,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
 
 class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "UnifiedGenotyper"
-  analysis_type = "UnifiedGenotyper"
+  def analysis_type = "UnifiedGenotyper"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -32,8 +32,7 @@ import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATK
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class VariantAnnotator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
-  analysisName = "VariantAnnotator"
-  analysis_type = "VariantAnnotator"
+  def analysis_type = "VariantAnnotator"
   scatterClass = classOf[LocusScatterFunction]
   setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -46,8 +46,7 @@ import org.broadinstitute.gatk.utils.commandline.Input
 import org.broadinstitute.gatk.utils.commandline.Output
 
 class VariantEval(val root: Configurable) extends CommandLineGATK {
-  analysisName = "VariantEval"
-  analysis_type = "VariantEval"
+  def analysis_type = "VariantEval"
 
   /** An output file created by the walker.  Will overwrite contents if file exists */
   @Output(fullName = "out", shortName = "o", doc = "An output file created by the walker.  Will overwrite contents if file exists", required = false, exclusiveOf = "", validation = "")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -52,8 +52,7 @@ import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, Tagg
 import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
 
 class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
-  analysisName = "VariantRecalibrator"
-  analysis_type = "VariantRecalibrator"
+  def analysis_type = "VariantRecalibrator"
 
   /** Recalibration mode to employ */
   @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ", required = true, exclusiveOf = "", validation = "")

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

@@ -15,17 +15,17 @@
  */
 package nl.lumc.sasc.biopet.core
 
-import java.io.{File, FileInputStream, PrintWriter}
+import java.io.{ File, FileInputStream, PrintWriter }
 import java.security.MessageDigest
 
 import nl.lumc.sasc.biopet.utils.Logging
-import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output }
 import org.broadinstitute.gatk.utils.runtime.ProcessSettings
 import org.ggf.drmaa.JobTemplate
 
 import scala.collection.mutable
 import scala.io.Source
-import scala.sys.process.{Process, ProcessLogger}
+import scala.sys.process.{ Process, ProcessLogger }
 import scala.collection.JavaConversions._
 
 /** Biopet command line trait to auto check executable and cluster values */