Rename old Gears to GearsSingle

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala

@@ -28,7 +28,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.carp.Carp,
     nl.lumc.sasc.biopet.pipelines.toucan.Toucan,
     nl.lumc.sasc.biopet.pipelines.shiva.ShivaSvCalling,
-    nl.lumc.sasc.biopet.pipelines.gears.Gears
+    nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
   )
 
   def pipelines: List[MainCommand] = List(

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala → public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala

@@ -28,7 +28,7 @@ import org.broadinstitute.gatk.queue.QScript
 /**
  * Created by wyleung
  */
-class Gears(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
+class GearsSingle(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
   def this() = this(null)
 
   @Input(doc = "R1 reads in FastQ format", shortName = "R1", required = false)
@@ -66,7 +66,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
   }
 
   override def reportClass = {
-    val gears = new GearsReport(this)
+    val gears = new GearsSingleReport(this)
     gears.outputDir = new File(outputDir, "report")
     gears.summaryFile = summaryFile
     sampleId.foreach(gears.args += "sampleId" -> _)
@@ -155,4 +155,4 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
 }
 
 /** This object give a default main method to the pipelines */
-object Gears extends PipelineCommand
\ No newline at end of file
+object GearsSingle extends PipelineCommand
\ No newline at end of file

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala → public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala

@@ -18,11 +18,11 @@ package nl.lumc.sasc.biopet.pipelines.gears
 import nl.lumc.sasc.biopet.core.report._
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
-class GearsReport(val root: Configurable) extends ReportBuilderExtension {
-  def builder = GearsReport
+class GearsSingleReport(val root: Configurable) extends ReportBuilderExtension {
+  def builder = GearsSingleReport
 }
 
-object GearsReport extends ReportBuilder {
+object GearsSingleReport extends ReportBuilder {
 
   // TODO: Add dustbin analysis (aggregated)
   // TODO: Add alignment stats per sample for the dustbin analysis

public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala → public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

@@ -31,14 +31,14 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations._
 
 /**
- * Test class for [[Gears]]
+ * Test class for [[GearsSingle]]
  *
  * Created by wyleung on 10/22/15.
  */
 
-class GearsPipelineTest(val testset: String) extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any]): Gears = {
-    new Gears {
+class GearsSingleTest(val testset: String) extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): GearsSingle = {
+    new GearsSingle {
       override def configName = "gears"
 
       override def globalConfig = new Config(map)
@@ -67,16 +67,16 @@ class GearsPipelineTest(val testset: String) extends TestNGSuite with Matchers {
   def testGears(testset: String, fromBam: Boolean, paired: Boolean,
                 hasOutputName: Boolean, hasFileExtension: Boolean) = {
     val map = ConfigUtils.mergeMaps(Map(
-      "output_dir" -> GearsTest.outputDir
-    ), Map(GearsTest.executables.toSeq: _*))
+      "output_dir" -> GearsSingleTest.outputDir
+    ), Map(GearsSingleTest.executables.toSeq: _*))
 
-    val gears: Gears = initPipeline(map)
+    val gears: GearsSingle = initPipeline(map)
 
     if (fromBam) {
-      gears.bamFile = if (hasFileExtension) Some(GearsTest.bam) else Some(GearsTest.bam_noext)
+      gears.bamFile = if (hasFileExtension) Some(GearsSingleTest.bam) else Some(GearsSingleTest.bam_noext)
     } else {
-      gears.fastqR1 = if (hasFileExtension) Some(GearsTest.r1) else Some(GearsTest.r1_noext)
-      gears.fastqR2 = if (paired) if (hasFileExtension) Some(GearsTest.r2) else Some(GearsTest.r2_noext) else None
+      gears.fastqR1 = if (hasFileExtension) Some(GearsSingleTest.r1) else Some(GearsSingleTest.r1_noext)
+      gears.fastqR2 = if (paired) if (hasFileExtension) Some(GearsSingleTest.r2) else Some(GearsSingleTest.r2_noext) else None
     }
     if (hasOutputName)
       gears.outputName = "test"
@@ -106,11 +106,11 @@ class GearsPipelineTest(val testset: String) extends TestNGSuite with Matchers {
 
   // remove temporary run directory all tests in the class have been run
   @AfterClass def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(GearsTest.outputDir)
+    FileUtils.deleteDirectory(GearsSingleTest.outputDir)
   }
 }
 
-object GearsTest {
+object GearsSingleTest {
   val outputDir = Files.createTempDir()
   new File(outputDir, "input").mkdirs()
 

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -27,7 +27,7 @@ import nl.lumc.sasc.biopet.extensions.{ Gsnap, Tophat, _ }
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
-import nl.lumc.sasc.biopet.pipelines.gears.Gears
+import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
 import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
@@ -259,7 +259,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     outputFiles += ("finalBamFile" -> finalBamFile.getAbsoluteFile)
 
     if (config("unmapped_to_gears", default = false).asBoolean) {
-      val gears = new Gears(this)
+      val gears = new GearsSingle(this)
       gears.bamFile = Some(finalBamFile)
       gears.outputDir = new File(outputDir, "gears")
       gears.init()