Change to config

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

@@ -18,10 +18,10 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   var input_R2: File = _
 
   @Argument(doc = "Skip Trim fastq files", shortName = "skiptrim", required = false)
-  var skipTrim: Boolean = false
+  var skipTrim: Boolean = config("skiptrim", default = false)
 
   @Argument(doc = "Skip Clip fastq files", shortName = "skipclip", required = false)
-  var skipClip: Boolean = false
+  var skipClip: Boolean = config("skipclip", default = false)
 
   @Argument(doc = "Sample name", shortName = "sample", required = true)
   var sampleName: String = _
@@ -43,8 +43,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   val summary = new FlexiprepSummary(this)
 
   def init() {
-    if (!skipTrim) skipTrim = config("skiptrim", default = false)
-    if (!skipClip) skipClip = config("skipclip", default = false)
     if (input_R1 == null) throw new IllegalStateException("Missing R1 on flexiprep module")
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
     if (sampleName == null) throw new IllegalStateException("Missing Sample name on flexiprep module")

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

@@ -18,18 +18,15 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
   @Input(doc = "Gvcf files", shortName = "I", required = false)
   var gvcfFiles: List[File] = Nil
 
-  @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = _
+  var reference: File = config("reference")
 
   @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
-  var dbsnp: File = _
+  var dbsnp: File = config("dbsnp")
 
   def init() {
     if (config.contains("gvcffiles")) for (file <- config("gvcffiles").getList) {
       gvcfFiles ::= file.toString
     }
-    if (reference == null) reference = config("reference")
-    if (dbsnp == null) dbsnp = config("dbsnp")
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
   }

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

@@ -13,10 +13,10 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
   var inputGvcfs: List[File] = Nil
 
   @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = _
+  var reference: File = config("reference")
 
   @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
-  var dbsnp: File = _
+  var dbsnp: File = config("dbsnp")
 
   @Argument(doc = "OutputName", required = false)
   var outputName: String = "genotype"
@@ -28,8 +28,6 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
   var samples: List[String] = Nil
 
   def init() {
-    if (reference == null) reference = config("reference")
-    if (dbsnp == null) dbsnp = config("dbsnp")
     if (outputFile == null) outputFile = outputDir + outputName + ".vcf.gz"
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
     else if (!outputDir.endsWith("/")) outputDir += "/"

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -27,17 +27,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   var mergeGvcfs: Boolean = false
 
   @Argument(doc = "Joint variantcalling", shortName = "jointVariantCalling", required = false)
-  var jointVariantcalling = false
+  var jointVariantcalling = config("joint_variantcalling", default = false)
 
   @Argument(doc = "Joint genotyping", shortName = "jointGenotyping", required = false)
-  var jointGenotyping = false
+  var jointGenotyping = config("joint_genotyping", default = false)
 
-  var singleSampleCalling = true
-  var reference: File = _
-  var dbsnp: File = _
+  var singleSampleCalling = config("single_sample_calling", default = true)
+  var reference: File = config("reference", required = true)
+  var dbsnp: File = config("dbsnp")
   var gvcfFiles: List[File] = Nil
   var finalBamFiles: List[File] = Nil
-  var useAllelesOption: Boolean = _
+  var useAllelesOption: Boolean = config("use_alleles_option", default = false)
 
   class LibraryOutput extends AbstractLibraryOutput {
     var mappedBamFile: File = _
@@ -49,15 +49,9 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   }
 
   def init() {
-    useAllelesOption = config("use_alleles_option", default = false)
-    reference = config("reference", required = true)
-    dbsnp = config("dbsnp")
     if (config.contains("target_bed")) {
       defaults ++= Map("gatk" -> Map(("intervals" -> config("target_bed").getStringList)))
     }
-    jointVariantcalling = config("joint_variantcalling", default = false)
-    jointGenotyping = config("joint_genotyping", default = false)
-    singleSampleCalling = config("single_sample_calling", default = true)
     if (config.contains("gvcfFiles"))
       for (file <- config("gvcfFiles").getList)
         gvcfFiles :+= file.toString

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

@@ -24,10 +24,10 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
   var rawVcfInput: File = _
 
   @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = _
+  var reference: File = config("reference", required = true)
 
   @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
-  var dbsnp: File = _
+  var dbsnp: File = config("dbsnp")
 
   @Argument(doc = "OutputName", required = false)
   var outputName: String = _
@@ -35,21 +35,14 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
   @Argument(doc = "Sample name", required = false)
   var sampleID: String = _
 
-  var preProcesBams: Option[Boolean] = None
+  var preProcesBams: Option[Boolean] = config("pre_proces_bams", default = true)
   var variantcalling: Boolean = true
-  var doublePreProces: Option[Boolean] = None
-  var useHaplotypecaller: Option[Boolean] = None
-  var useUnifiedGenotyper: Option[Boolean] = None
-  var useAllelesOption: Option[Boolean] = None
+  var doublePreProces: Option[Boolean] = config("double_pre_proces", default = true)
+  var useHaplotypecaller: Option[Boolean] = config("use_haplotypecaller", default = true)
+  var useUnifiedGenotyper: Option[Boolean] = config("use_unifiedgenotyper", default = false)
+  var useAllelesOption: Option[Boolean] = config("use_alleles_option", default = false)
 
   def init() {
-    if (useAllelesOption == None) useAllelesOption = config("use_alleles_option", default = false)
-    if (preProcesBams == None) preProcesBams = config("pre_proces_bams", default = true)
-    if (doublePreProces == None) doublePreProces = config("double_pre_proces", default = true)
-    if (useHaplotypecaller == None) useHaplotypecaller = config("use_haplotypecaller", default = true)
-    if (useUnifiedGenotyper == None) useUnifiedGenotyper = config("use_unifiedgenotyper", default = false)
-    if (reference == null) reference = config("reference", required = true)
-    if (dbsnp == null) dbsnp = config("dbsnp")
     if (outputName == null && sampleID != null) outputName = sampleID
     else if (outputName == null) outputName = "noname"
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala

@@ -16,7 +16,7 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
   var vcfFiles: List[File] = _
 
   @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = _
+  var reference: File = config("reference")
 
   @Argument(doc = "Target bed", shortName = "targetBed", required = false)
   var targetBed: List[File] = Nil
@@ -29,7 +29,6 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
   def generalSampleDir = outputDir + "samples/"
 
   def init() {
-    if (reference == null) reference = config("reference")
     if (config.contains("target_bed"))
       for (bed <- config("target_bed").getList)
         targetBed :+= bed.toString