Commit 3c616b75 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Moved scripts to general package

parent f3276d72
package nl.lumc.sasc.biopet.pipelines.bammetrics package nl.lumc.sasc.biopet.pipelines.bammetrics
import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats import nl.lumc.sasc.biopet.scripts.CoverageStats
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand } import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import java.io.File import java.io.File
......
...@@ -6,7 +6,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument } ...@@ -6,7 +6,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand } import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.{ Gzip, Pbzip2, Md5sum, Zcat } import nl.lumc.sasc.biopet.extensions.{ Gzip, Pbzip2, Md5sum, Zcat }
import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._ import nl.lumc.sasc.biopet.scripts._
class Flexiprep(val root: Configurable) extends QScript with BiopetQScript { class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null) def this() = this(null)
......
...@@ -3,8 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep ...@@ -3,8 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.PrintWriter import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.Md5sum import nl.lumc.sasc.biopet.extensions.Md5sum
import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.{ FastqSync, Seqstat } import nl.lumc.sasc.biopet.scripts.{ FastqSync, Seqstat }
import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.Seqstat
import org.broadinstitute.gatk.queue.function.InProcessFunction import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output } import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File import java.io.File
......
package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts package nl.lumc.sasc.biopet.scripts
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
......
package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts package nl.lumc.sasc.biopet.scripts
import java.io.File import java.io.File
......
package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts package nl.lumc.sasc.biopet.scripts
import java.io.File import java.io.File
......
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