Commit 99f18f74 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Rename pipelines

parent 9c83fc47
......@@ -9,17 +9,17 @@ import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 2/26/15.
*/
class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
class Shiva(val root: Configurable) extends QScript with ShivaTrait {
qscript =>
def this() = this(null)
override def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
if (multisample) new ShivaVariantcallingGatk(qscript) {
if (multisample) new ShivaVariantcalling(qscript) {
override def namePrefix = "multisample"
override def configName = "shivavariantcalling"
override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
}
else new ShivaVariantcallingGatk(qscript) {
else new ShivaVariantcalling(qscript) {
override def configName = "shivavariantcalling"
}
}
......@@ -47,9 +47,9 @@ class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
}
}
override def doublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
if (input.size <= 1) super.doublePreProcess(input)
else super.doublePreProcess(input, true).collect {
override protected def addDoublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
if (input.size <= 1) super.addDoublePreProcess(input)
else super.addDoublePreProcess(input, true).collect {
case file => {
config("use_indel_realign", default = true).asBoolean match {
case true => addIndelRealign(file, sampleDir, false)
......@@ -98,4 +98,4 @@ class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
}
}
object ShivaGatk extends PipelineCommand
\ No newline at end of file
object Shiva extends PipelineCommand
\ No newline at end of file
......@@ -9,7 +9,7 @@ import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 2/26/15.
*/
class ShivaVariantcallingGatk(val root: Configurable) extends QScript with ShivaVariantcallingTrait {
class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVariantcallingTrait {
qscript =>
def this() = this(null)
......@@ -104,4 +104,4 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
}
}
object ShivaVariantcallingGatk extends PipelineCommand
\ No newline at end of file
object ShivaVariantcalling extends PipelineCommand
\ No newline at end of file
......@@ -15,11 +15,11 @@ import org.testng.annotations.{ Test, DataProvider }
/**
* Created by pjvan_thof on 3/2/15.
*/
class ShivaGatkTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): ShivaGatk = {
new ShivaGatk() {
class ShivaTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Shiva = {
new Shiva() {
override def configName = "shiva"
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaGatkTest.config))
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaTest.config))
qSettings = new QSettings
qSettings.runName = "test"
}
......@@ -40,10 +40,10 @@ class ShivaGatkTest extends TestNGSuite with Matchers {
multi: Boolean, single: Boolean, library: Boolean, dbsnp: Boolean,
covariates: Boolean, realign: Boolean, baseRecalibration: Boolean): Unit = {
val map = {
var m: Map[String, Any] = ShivaGatkTest.config
if (sample1) m = ConfigUtils.mergeMaps(ShivaGatkTest.sample1, m.toMap)
if (sample2) m = ConfigUtils.mergeMaps(ShivaGatkTest.sample2, m.toMap)
if (sample3) m = ConfigUtils.mergeMaps(ShivaGatkTest.sample3, m.toMap)
var m: Map[String, Any] = ShivaTest.config
if (sample1) m = ConfigUtils.mergeMaps(ShivaTest.sample1, m.toMap)
if (sample2) m = ConfigUtils.mergeMaps(ShivaTest.sample2, m.toMap)
if (sample3) m = ConfigUtils.mergeMaps(ShivaTest.sample3, m.toMap)
if (dbsnp) m = ConfigUtils.mergeMaps(Map("dbsnp" -> "test"), m.toMap)
ConfigUtils.mergeMaps(Map("multisample_sample_variantcalling" -> multi,
"single_sample_variantcalling" -> single,
......@@ -80,7 +80,7 @@ class ShivaGatkTest extends TestNGSuite with Matchers {
}
}
object ShivaGatkTest {
object ShivaTest {
val outputDir = Files.createTempDir()
val config = Map(
......
......@@ -19,11 +19,11 @@ import scala.collection.mutable.ListBuffer
/**
* Created by pjvan_thof on 3/2/15.
*/
class ShivaVariantcallingGatkTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): ShivaVariantcallingGatk = {
new ShivaVariantcallingGatk() {
class ShivaVariantcallingTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): ShivaVariantcalling = {
new ShivaVariantcalling() {
override def configName = "shivavariantcalling"
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingGatkTest.config))
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config))
qSettings = new QSettings
qSettings.runName = "test"
}
......@@ -94,11 +94,11 @@ class ShivaVariantcallingGatkTest extends TestNGSuite with Matchers {
}
@AfterClass def removeTempOutputDir() = {
FileUtils.deleteDirectory(ShivaVariantcallingGatkTest.outputDir)
FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
}
}
object ShivaVariantcallingGatkTest {
object ShivaVariantcallingTest {
val outputDir = Files.createTempDir()
val config = Map(
......
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