autogenerated styles

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

@@ -94,7 +94,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
       if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
       else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
     }
-    
+
     this match {
       case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
         logger.info("Write report is skipped because sample flag is used")

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala

 package nl.lumc.sasc.biopet.extensions.manwe
 
-
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{Output, Argument}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Argument }
 
 /**
  * Created by ahbbollen on 23-9-15.
@@ -17,7 +16,7 @@ abstract class Manwe extends BiopetCommandLineFunction {
   override def defaultCoreMemory = 2.0
   override def defaultThreads = 1
 
-  @Argument(doc="Path to manwe config file containing your database settings", required = true)
+  @Argument(doc = "Path to manwe config file containing your database settings", required = true)
   var manweConfig: Option[File] = config("manwe_config")
 
   @Output(doc = "the output file")
@@ -25,15 +24,15 @@ abstract class Manwe extends BiopetCommandLineFunction {
 
   var manweHelp: Boolean = false
 
-  def subCommand : String
+  def subCommand: String
 
   final def cmdLine = {
     required(executable) +
-    subCommand +
-    required("-c", manweConfig) +
-    conditional(manweHelp, "-h") +
-    " > " +
-    required(output)
+      subCommand +
+      required("-c", manweConfig) +
+      conditional(manweHelp, "-h") +
+      " > " +
+      required(output)
   }
 
   /**

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Argument}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
 
 /**
  * Created by ahbbollen on 24-9-15.

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
 
 /**
  * Created by ahbbollen on 24-9-15.
@@ -21,11 +21,8 @@ class ManweAnnotateVcf(val root: Configurable) extends Manwe {
 
   def subCommand = {
     required("annotate-vcf") + required(vcf) +
-    conditional(alreadyUploaded, "-u") +
-    repeat("-q", queries)
+      conditional(alreadyUploaded, "-u") +
+      repeat("-q", queries)
   }
 
-
-
-
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala

@@ -16,9 +16,7 @@ class ManweDataSourcesAnnotate(val root: Configurable) extends Manwe {
 
   def subCommand = {
     required("data-sources") + required("annotate") +
-    required(uri) + repeat("-q", queries)
+      required(uri) + repeat("-q", queries)
   }
 
-
-
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 24-9-15.
@@ -15,10 +15,8 @@ class ManweDataSourcesList(val root: Configurable) extends Manwe {
 
   def subCommand = {
     required("data-sources") + required("list") +
-    optional("-u", user)
+      optional("-u", user)
   }
 
-
 }
 
-

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 24-9-15.
@@ -11,11 +11,11 @@ import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
 class ManweDataSourcesShow(val root: Configurable) extends Manwe {
 
   @Argument(doc = "uri of data source")
-  var uri:  Option[String] = _
+  var uri: Option[String] = _
 
   def subCommand = {
     required("data-sources") + required("show") +
-    required(uri)
+      required(uri)
   }
 
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 24-9-15.
@@ -15,8 +15,7 @@ class ManweSamplesActivate(val root: Configurable) extends Manwe {
 
   def subCommand = {
     required("samples") + required("activate") +
-    required(uri)
+      required(uri)
   }
 
-
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 24-9-15.
@@ -21,10 +21,7 @@ class ManweSamplesAdd(val root: Configurable) extends Manwe {
 
   def subCommand = {
     required("samples") + required("add") + required(name) +
-    optional("-s", poolSize) + repeat("-g", group)
+      optional("-s", poolSize) + repeat("-g", group)
   }
 
-
-
-
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala

@@ -3,15 +3,14 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 24-9-15.
  */
 class ManweSamplesAnnotateVariations(val root: Configurable) extends Manwe {
 
-
-  @Argument(doc= "uri to sample to annotate")
+  @Argument(doc = "uri to sample to annotate")
   var uri: Option[String] = _
 
   @Argument(doc = "Annotation queries")
@@ -19,10 +18,7 @@ class ManweSamplesAnnotateVariations(val root: Configurable) extends Manwe {
 
   def subCommand = {
     required("samples") + required("annotate-variations") +
-    required(uri) + repeat("-q", queries)
+      required(uri) + repeat("-q", queries)
   }
 
-
-
-
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 24-9-15.
@@ -39,18 +39,14 @@ class ManweSamplesImport(val root: Configurable) extends Manwe {
   var preferLikelihood: Boolean = false
 
   @Argument(doc = "Pool size")
-  var poolSize : Option[Int] = _
+  var poolSize: Option[Int] = _
 
   def subCommand = {
     required("samples") + required("import") + required(name) +
-    repeat("-g", group) + repeat("--vcf", vcfs) + repeat("--bed", beds) +
-    optional("-s", poolSize) + conditional(alreadyUploaded, "-u") +
-    conditional(public, "-p") + conditional(preferLikelihood, "-l") +
-    conditional(noCoverage, "--no-coverage-profile")
+      repeat("-g", group) + repeat("--vcf", vcfs) + repeat("--bed", beds) +
+      optional("-s", poolSize) + conditional(alreadyUploaded, "-u") +
+      conditional(public, "-p") + conditional(preferLikelihood, "-l") +
+      conditional(noCoverage, "--no-coverage-profile")
   }
 
-
-
-
-
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 24-9-15.
@@ -20,8 +20,7 @@ class ManweSamplesImportBed(val root: Configurable) extends Manwe {
   @Argument(doc = "path to VCF file to upload")
   var bed: File = _
 
-  @Argument(doc = "flag if data is already uploaded?")
-  // TODO: What is the use of this flag even? We're specifically uploading with this command
+  @Argument(doc = "flag if data is already uploaded?") // TODO: What is the use of this flag even? We're specifically uploading with this command
   var alreadyUploaded: Boolean = false
 
   def subCommand = {

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 24-9-15.
@@ -20,8 +20,7 @@ class ManweSamplesImportVcf(val root: Configurable) extends Manwe {
   @Argument(doc = "path to VCF file to upload")
   var vcf: File = _
 
-  @Argument(doc = "flag if data is already uploaded?")
-  // TODO: What is the use of this flag even? We're specifically uploading with this command
+  @Argument(doc = "flag if data is already uploaded?") // TODO: What is the use of this flag even? We're specifically uploading with this command
   var alreadyUploaded: Boolean = false
 
   @Argument(doc = "Flag when to prefer genotype likelihoods")
@@ -29,8 +28,8 @@ class ManweSamplesImportVcf(val root: Configurable) extends Manwe {
 
   def subCommand = {
     required("samples") + required("import-vcf") +
-    required(uri) + required(vcf) +
-    conditional(alreadyUploaded, "-u") + conditional(preferLikelihoods, "-l")
+      required(uri) + required(vcf) +
+      conditional(alreadyUploaded, "-u") + conditional(preferLikelihoods, "-l")
   }
 
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 23-9-15.
@@ -20,12 +20,7 @@ class ManweSamplesList(val root: Configurable) extends Manwe {
 
   def subCommand = {
     required("samples") + required("list") + optional("-u", user) +
-    repeat("-g", group) + conditional(onlyPublic, "-p")
+      repeat("-g", group) + conditional(onlyPublic, "-p")
   }
 
-
-
-
-
-
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
  * Created by ahbbollen on 24-9-15.