Commit a0573985 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add deprication tag

parent 502bfac1
......@@ -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"
......
......@@ -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
......
......@@ -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"
......
......@@ -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 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)
......
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