Commit 43fc01cd authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Move SVcallers into the toplevel extensions directory

parent 0f475cfa
...@@ -13,16 +13,14 @@ ...@@ -13,16 +13,14 @@
* license; For commercial users or users who do not want to follow the AGPL * license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license. * license, please contact us to obtain a separate license.
*/ */
package nl.lumc.sasc.biopet.extensions.svcallers package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File import java.io.File
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.BiopetQScript import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.PipelineCommand import nl.lumc.sasc.biopet.extensions.breakdancer.BreakdancerVCF
import org.broadinstitute.gatk.queue.QScript
/// Breakdancer is actually a mini pipeline executing binaries from the breakdancer package /// Breakdancer is actually a mini pipeline executing binaries from the breakdancer package
class Breakdancer(val root: Configurable) extends QScript with BiopetQScript { class Breakdancer(val root: Configurable) extends QScript with BiopetQScript {
......
package nl.lumc.sasc.biopet.extensions.svcallers package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction { class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "breakdancer-max", freeVar = false) executable = config("exe", default = "breakdancer-max", freeVar = false)
......
package nl.lumc.sasc.biopet.extensions.svcallers package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerConfig(val root: Configurable) extends BiopetCommandLineFunction { class BreakdancerConfig(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "bam2cfg.pl", freeVar = false) executable = config("exe", default = "bam2cfg.pl", freeVar = false)
......
...@@ -13,14 +13,13 @@ ...@@ -13,14 +13,13 @@
* license; For commercial users or users who do not want to follow the AGPL * license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license. * license, please contact us to obtain a separate license.
*/ */
package nl.lumc.sasc.biopet.extensions.svcallers package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction { class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
setPythonScript("breakdancer2vcf.py") setPythonScript("breakdancer2vcf.py")
......
...@@ -13,16 +13,13 @@ ...@@ -13,16 +13,13 @@
* license; For commercial users or users who do not want to follow the AGPL * license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license. * license, please contact us to obtain a separate license.
*/ */
package nl.lumc.sasc.biopet.extensions.svcallers package nl.lumc.sasc.biopet.extensions.clever
import java.io.File import java.io.File
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.BiopetQScript import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.PipelineCommand import org.broadinstitute.gatk.queue.QScript
class Clever(val root: Configurable) extends QScript with BiopetQScript { class Clever(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null) def this() = this(null)
......
package nl.lumc.sasc.biopet.extensions.svcallers package nl.lumc.sasc.biopet.extensions.clever
import java.io.File import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction { class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "clever") executable = config("exe", default = "clever")
......
package nl.lumc.sasc.biopet.extensions.svcallers package nl.lumc.sasc.biopet.extensions.delly
import java.io.File import java.io.File
......
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL * license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license. * license, please contact us to obtain a separate license.
*/ */
package nl.lumc.sasc.biopet.extensions.svcallers.pindel package nl.lumc.sasc.biopet.extensions.pindel
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
......
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL * license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license. * license, please contact us to obtain a separate license.
*/ */
package nl.lumc.sasc.biopet.extensions.svcallers.pindel package nl.lumc.sasc.biopet.extensions.pindel
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
......
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL * license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license. * license, please contact us to obtain a separate license.
*/ */
package nl.lumc.sasc.biopet.extensions.svcallers.pindel package nl.lumc.sasc.biopet.extensions.pindel
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.PipelineCommand import nl.lumc.sasc.biopet.core.PipelineCommand
......
...@@ -25,10 +25,12 @@ import nl.lumc.sasc.biopet.core.config.Configurable ...@@ -25,10 +25,12 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, MultiSampleQScript, PipelineCommand } import nl.lumc.sasc.biopet.core.{ BiopetQScript, MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.Ln import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaMerge, SambambaMarkdup } import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaMerge, SambambaMarkdup }
//import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel //import nl.lumc.sasc.biopet.extensions.pindel.Pindel
import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Delly, CleverCaller } import nl.lumc.sasc.biopet.extensions.delly.Delly
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
......
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