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Commit c4c8292b authored by Peter van 't Hof's avatar Peter van 't Hof
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Move abstract commandlines function for Rscript and Python

parent 806133cd
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Inline Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala → public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
View file @ c4c8292b
......@@ -13,9 +13,9 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions
package nl.lumc.sasc.biopet.core.extensions
import java.io.{ File, FileOutputStream }
import java.io.{File, FileOutputStream}
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.Input
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala → public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
View file @ c4c8292b
......@@ -13,9 +13,9 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions
package nl.lumc.sasc.biopet.core.extensions
import java.io.{ File, FileOutputStream }
import java.io.{File, FileOutputStream}
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
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......@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
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......@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.extensions.conifer
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
abstract class Conifer extends PythonCommandLineFunction {
override def subPath = "conifer" :: super.subPath
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
View file @ c4c8292b
......@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import java.io.File
import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
View file @ c4c8292b
......@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import java.io.File
import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
View file @ c4c8292b
......@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import java.io.File
import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
View file @ c4c8292b
......@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.scripts
import java.io.File
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
......
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