Commit 431621b2 authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent 0f03cdf4
...@@ -14,20 +14,20 @@ ...@@ -14,20 +14,20 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.gentrap package nl.lumc.sasc.biopet.pipelines.gentrap
import java.io.{File, FileOutputStream} import java.io.{ File, FileOutputStream }
import com.google.common.io.Files import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, BiopetPipe} import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetPipe }
import nl.lumc.sasc.biopet.extensions._ import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import nl.lumc.sasc.biopet.extensions.tools.{BaseCounter, WipeReads} import nl.lumc.sasc.biopet.extensions.tools.{ BaseCounter, WipeReads }
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging} import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{DataProvider, Test} import org.testng.annotations.{ DataProvider, Test }
abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends TestNGSuite with Matchers { abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends TestNGSuite with Matchers {
...@@ -68,14 +68,14 @@ abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends ...@@ -68,14 +68,14 @@ abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends
aligner.map("aligner" -> _) ++ aligner.map("aligner" -> _) ++
removeRiboReads.map("remove_ribosomal_reads" -> _) removeRiboReads.map("remove_ribosomal_reads" -> _)
val configs: List[Option[Map[String, Any]]] = List(Some(settings), (if (sample1) Some(GentrapTest.sample1) else None), (if (sample2) Some(GentrapTest.sample2) else None)) val configs: List[Option[Map[String, Any]]] = List(Some(settings), (if (sample1) Some(GentrapTest.sample1) else None), (if (sample2) Some(GentrapTest.sample2) else None))
val config = configs.flatten.foldLeft(GentrapTest.executables)( (a,b) => ConfigUtils.mergeMaps(a, b)) val config = configs.flatten.foldLeft(GentrapTest.executables)((a, b) => ConfigUtils.mergeMaps(a, b))
val gentrap: Gentrap = initPipeline(config) val gentrap: Gentrap = initPipeline(config)
val numSamples = (sample1, sample2) match { val numSamples = (sample1, sample2) match {
case (true, true) => 2 case (true, true) => 2
case (_, true) => 1 case (_, true) => 1
case (true, _) => 1 case (true, _) => 1
case _ => 0 case _ => 0
} }
if (numSamples == 0) { if (numSamples == 0) {
...@@ -88,8 +88,8 @@ abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends ...@@ -88,8 +88,8 @@ abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends
val functions = gentrap.functions.flatMap { val functions = gentrap.functions.flatMap {
case f: BiopetFifoPipe => f.pipesJobs case f: BiopetFifoPipe => f.pipesJobs
case f: BiopetPipe => f.pipesJobs case f: BiopetPipe => f.pipesJobs
case f => List(f) case f => List(f)
}.groupBy(_.getClass) }.groupBy(_.getClass)
if (expressionMeasures.contains("fragments_per_gene")) if (expressionMeasures.contains("fragments_per_gene"))
......
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