Commit 973753d8 authored by Peter van 't Hof's avatar Peter van 't Hof

Rename to download genomes

parent 0dffdd00
......@@ -14,7 +14,7 @@
*/
package nl.lumc.sasc.biopet
import nl.lumc.sasc.biopet.pipelines.generateindexes.GenerateIndexes
import nl.lumc.sasc.biopet.pipelines.generateindexes.DownloadGenomes$
import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
object BiopetExecutableMain extends BiopetExecutable {
......@@ -38,7 +38,7 @@ 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,
GenerateIndexes
DownloadGenomes
)
def tools: List[MainCommand] = BiopetToolsExecutable.tools
......
......@@ -33,7 +33,7 @@ import org.broadinstitute.gatk.queue.QScript
import scala.collection.JavaConversions._
import scala.language.reflectiveCalls
class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript {
class DownloadGenomes(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
@Argument(required = true)
......@@ -327,4 +327,4 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
}
}
object GenerateIndexes extends PipelineCommand
object DownloadGenomes extends PipelineCommand
......@@ -25,11 +25,11 @@ import org.testng.annotations.Test
/**
* Created by pjvan_thof on 13-5-16.
*/
class GenerateIndexesTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): GenerateIndexes = {
new GenerateIndexes() {
class DownloadGenomesTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): DownloadGenomes = {
new DownloadGenomes() {
override def configNamespace = "generateindexes"
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, GenerateIndexesTest.config))
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, DownloadGenomesTest.config))
qSettings = new QSettings
qSettings.runName = "test"
}
......@@ -116,7 +116,7 @@ class GenerateIndexesTest extends TestNGSuite with Matchers {
}
object GenerateIndexesTest {
object DownloadGenomesTest {
val outputDir = Files.createTempDir()
outputDir.deleteOnExit()
......
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