Add deprication tag

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

@@ -25,6 +25,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output }
  * Extension for CombineVariants from GATK
  *
  * Created by pjvan_thof on 2/26/15.
+ *
+ * @deprecated
  */
 class CombineVariants(val root: Configurable) extends Gatk {
   val analysisType = "CombineVariants"

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala

@@ -24,6 +24,8 @@ import org.broadinstitute.gatk.utils.commandline.Input
  * General extension for GATK module
  *
  * Created by pjvan_thof on 2/26/15.
+ *
+ * @deprecated
  */
 abstract class Gatk extends BiopetJavaCommandLineFunction with Reference with Version {
   override def subPath = "gatk" :: super.subPath

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala

@@ -26,6 +26,8 @@ import org.broadinstitute.gatk.utils.report.{ GATKReportTable, GATKReport }
  * Extension for CombineVariants from GATK
  *
  * Created by pjvan_thof on 2/26/15.
+ *
+ * @deprecated
  */
 class GenotypeConcordance(val root: Configurable) extends Gatk with Summarizable {
   val analysisType = "GenotypeConcordance"

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

@@ -25,6 +25,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output }
  * Extension for CombineVariants from GATK
  *
  * Created by pjvan_thof on 2/26/15.
+ *
+ * @deprecated
  */
 class SelectVariants(val root: Configurable) extends Gatk {
   val analysisType = "SelectVariants"

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

-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
 
+/**
+ * @deprecated
+ */
 trait GatkGeneral extends org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK with CommandLineResources with Reference with Version {
   var executable: String = config("java", default = "java", namespace = "java", freeVar = false)