Commit 9f83974b authored by Peter van 't Hof's avatar Peter van 't Hof

Moved package

parent f737d360
......@@ -15,7 +15,8 @@
*/
package nl.lumc.sasc.biopet
import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
import nl.lumc.sasc.biopet.pipelines.generateindexes.GenerateIndexes
import nl.lumc.sasc.biopet.utils.{BiopetExecutable, MainCommand}
object BiopetExecutableMain extends BiopetExecutable {
def pipelines: List[MainCommand] = List(
......@@ -36,7 +37,7 @@ object BiopetExecutableMain extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
nl.lumc.sasc.biopet.pipelines.basty.Basty,
nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
nl.lumc.sasc.biopet.pipelines.GenerateIndexes
GenerateIndexes
)
def tools: List[MainCommand] = BiopetToolsExecutable.tools
......
......@@ -13,26 +13,26 @@
* 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.pipelines
package nl.lumc.sasc.biopet.pipelines.generateindexes
import java.io.PrintWriter
import java.util
import nl.lumc.sasc.biopet.core.extensions.Md5sum
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, BiopetQScript, PipelineCommand}
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2Build, BowtieBuild }
import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie2Build, BowtieBuild}
import nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.gmap.GmapBuild
import nl.lumc.sasc.biopet.extensions.picard.CreateSequenceDictionary
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFaidx
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import scala.language.reflectiveCalls
import scala.collection.JavaConversions._
import scala.language.reflectiveCalls
class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment