Biopet core code inspection round

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala

@@ -43,7 +43,7 @@ class PrefixFastq(val parent: Configurable) extends ToolCommandFunction {
     * Creates command to execute extension
     * @return
     */
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-i", inputFastq) +
       required("-o", outputFastq) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala

@@ -31,7 +31,7 @@ class SageCountFastq(val parent: Configurable) extends ToolCommandFunction {
 
   override def defaultCoreMemory = 3.0
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-I", input) +
       required("-o", output)

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala

@@ -38,12 +38,12 @@ class SageCreateLibrary(val parent: Configurable) extends ToolCommandFunction {
   @Output(doc = "Output file all genes", shortName = "allGenes", required = false)
   var allGenesOutput: File = _
 
-  var tag: String = config("tag", default = "CATG")
-  var length: Option[Int] = config("length", default = 17)
+  val tag: String = config("tag", default = "CATG")
+  val length: Option[Int] = config("length", default = 17)
 
   override def defaultCoreMemory = 3.0
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-I", input) +
       optional("--tag", tag) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala

@@ -43,7 +43,7 @@ class SageCreateTagCounts(val parent: Configurable) extends ToolCommandFunction
 
   override def defaultCoreMemory = 3.0
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-I", input) +
       required("--tagLib", tagLib) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala

@@ -33,14 +33,14 @@ class SeqStat(val parent: Configurable) extends ToolCommandFunction with Summari
   mainFunction = false
 
   @Input(doc = "Input FASTQ", shortName = "input", required = true)
-  var input: File = null
+  var input: File = _
 
   @Output(doc = "Output JSON", shortName = "output", required = true)
-  var output: File = null
+  var output: File = _
 
   override def defaultCoreMemory = 4.0
 
-  override def cmdLine = super.cmdLine + required("-i", input) + required("-o", output)
+  override def cmdLine: String = super.cmdLine + required("-i", input) + required("-o", output)
 
   def summaryStats: Map[String, Any] = {
     val map = ConfigUtils.fileToConfigMap(output)

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala

@@ -28,7 +28,7 @@ class SnptestToVcf(val parent: Configurable) extends ToolCommandFunction with Re
   def toolObject = nl.lumc.sasc.biopet.tools.SnptestToVcf
 
   @Input(doc = "input Info file", required = true)
-  var inputInfo: File = null
+  var inputInfo: File = _
 
   @Input(required = true)
   var reference: File = _
@@ -45,7 +45,7 @@ class SnptestToVcf(val parent: Configurable) extends ToolCommandFunction with Re
     //if (outputVcf.getName.endsWith(".vcf.gz")) outputFiles :+= new File(outputVcf.getAbsolutePath + ".tbi")
   }
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("--inputInfo", inputInfo) +
       required("--outputVcf", outputVcf) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala

@@ -32,9 +32,9 @@ class SquishBed(val parent: Configurable) extends ToolCommandFunction {
   @Output(doc = "Output interval list", required = true)
   var output: File = _
 
-  var strandSensitive: Boolean = config("strandSensitive", default = false)
+  val strandSensitive: Boolean = config("strandSensitive", default = false)
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-I", input) +
       required("-o", output) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateAnnotation.scala

@@ -41,7 +41,7 @@ class ValidateAnnotation(val parent: Configurable) extends ToolCommandFunction w
     if (reference == null) reference = referenceFasta()
   }
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       optional("-r", refflatFile) +
       repeat("-g", gtfFile) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala

@@ -31,7 +31,7 @@ class ValidateFastq(val parent: Configurable) extends ToolCommandFunction {
 
   override def defaultCoreMemory = 4.0
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-i", r1Fastq) +
       optional("-j", r2Fastq)

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateVcf.scala

@@ -38,7 +38,7 @@ class ValidateVcf(val parent: Configurable) extends ToolCommandFunction with Ref
     if (reference == null) reference = referenceFasta()
   }
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-i", inputVcf) +
       required("-R", reference) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala

@@ -61,7 +61,7 @@ class VcfFilter(val parent: Configurable) extends ToolCommandFunction {
       outputVcfIndex = new File(outputVcf.getAbsolutePath + ".tbi")
   }
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-I", inputVcf) +
       required("-o", outputVcf) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala

@@ -50,9 +50,9 @@ class VcfStats(val parent: Configurable)
   protected var outputDir: File = _
 
   var infoTags: List[String] = Nil
-  var genotypeTags: List[String] = Nil
-  var allInfoTags = false
-  var allGenotypeTags = false
+  val genotypeTags: List[String] = Nil
+  val allInfoTags = false
+  val allGenotypeTags = false
   var reference: File = _
   var intervals: Option[File] = None
 

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala

@@ -39,7 +39,7 @@ class VcfStatsForSv(val parent: Configurable) extends ToolCommandFunction with S
   override def defaultResidentFactor = 2.0
   override def defaultVmemFactor = 3.0
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-i", inputFile) +
       required("-o", outputFile) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala

@@ -53,7 +53,7 @@ class VcfWithVcf(val parent: Configurable) extends ToolCommandFunction with Refe
     if (fields.isEmpty) throw new IllegalArgumentException("No fields found for VcfWithVcf")
   }
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-I", input) +
       required("-o", output) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala

@@ -33,17 +33,17 @@ class VepNormalizer(val parent: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.VepNormalizer
 
   @Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
-  var inputVCF: File = null
+  var inputVCF: File = _
 
   @Output(doc = "Output VCF", shortName = "OutputFile", required = true)
-  var outputVcf: File = null
+  var outputVcf: File = _
 
-  var mode: String = config("mode", default = "standard")
-  var doNotRemove: Boolean = config("do_not_remove", default = false)
+  val mode: String = config("mode", default = "standard")
+  val doNotRemove: Boolean = config("do_not_remove", default = false)
 
   override def defaultCoreMemory = 4.0
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-I", inputVCF) +
       required("-O", outputVcf) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala

@@ -30,35 +30,35 @@ class WipeReads(val parent: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.WipeReads
 
   @Input(doc = "Input BAM file (must be indexed)", shortName = "I", required = true)
-  var inputBam: File = null
+  var inputBam: File = _
 
   @Input(doc = "Interval file", shortName = "r", required = true)
-  var intervalFile: File = null
+  var intervalFile: File = _
 
   @Argument(doc = "Minimum MAPQ of reads in target region to remove (default: 0)")
-  var minMapQ: Option[Int] = config("min_mapq")
+  val minMapQ: Option[Int] = config("min_mapq")
 
   @Argument(doc = "Read group IDs to be removed (default: remove reads from all read groups)")
-  var readgroup: Set[String] = config("read_group", default = Nil)
+  val readgroup: Set[String] = config("read_group", default = Nil)
 
   @Argument(
     doc = "Whether to remove multiple-mapped reads outside the target regions (default: yes)")
-  var limitRemoval: Boolean = config("limit_removal", default = false)
+  val limitRemoval: Boolean = config("limit_removal", default = false)
 
   @Argument(doc = "Whether to index output BAM file or not")
-  var noMakeIndex: Boolean = config("no_make_index", default = false)
+  val noMakeIndex: Boolean = config("no_make_index", default = false)
 
   @Argument(doc = "GTF feature containing intervals (default: exon)")
-  var featureType: Option[String] = config("feature_type")
+  val featureType: Option[String] = config("feature_type")
 
   @Argument(doc = "Expected maximum number of reads in target regions (default: 7e7)")
-  var bloomSize: Option[Long] = config("bloom_size")
+  val bloomSize: Option[Long] = config("bloom_size")
 
   @Argument(doc = "False positive rate (default: 4e-7)")
-  var falsePositive: Option[Long] = config("false_positive")
+  val falsePositive: Option[Long] = config("false_positive")
 
   @Output(doc = "Output BAM", shortName = "o", required = true)
-  var outputBam: File = null
+  var outputBam: File = _
 
   @Output(required = false)
   private var outputIndex: Option[File] = None
@@ -71,7 +71,7 @@ class WipeReads(val parent: Configurable) extends ToolCommandFunction {
     if (!noMakeIndex) outputIndex = Some(new File(outputBam.getPath.stripSuffix(".bam") + ".bai"))
   }
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-I", inputBam) +
       required("-r", intervalFile) +

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala

@@ -37,7 +37,7 @@ class XcnvToBed(val parent: Configurable) extends ToolCommandFunction {
 
   override def defaultCoreMemory = 4
 
-  override def cmdLine = {
+  override def cmdLine: String = {
     super.cmdLine + required("-I", inputXcnv) + required("-O", outpuBed) + required("-S", sample)
   }
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala

@@ -24,7 +24,7 @@ import org.testng.annotations.Test
 class BiopetPipeTest extends TestNGSuite with Matchers {
   class Pipe1 extends BiopetCommandLineFunction {
     val parent = null
-    def cmdLine =
+    def cmdLine: String =
       "pipe1" +
         (if (!inputAsStdin) " input1 " else "") +
         (if (!outputAsStdout) " output1 " + "")
@@ -32,13 +32,13 @@ class BiopetPipeTest extends TestNGSuite with Matchers {
 
   class Pipe2 extends BiopetCommandLineFunction {
     val parent = null
-    def cmdLine =
+    def cmdLine: String =
       "pipe2" +
         (if (!inputAsStdin) " input2 " else "") +
         (if (!outputAsStdout) " output2 " + "")
   }
 
-  @Test def testPipeCommands: Unit = {
+  @Test def testPipeCommands(): Unit = {
     val pipe1 = new Pipe1
     val pipe2 = new Pipe2
     pipe1.commandLine.contains("pipe1") shouldBe true
@@ -49,7 +49,7 @@ class BiopetPipeTest extends TestNGSuite with Matchers {
     pipe2.commandLine.contains("output2") shouldBe true
   }
 
-  @Test def testPipe: Unit = {
+  @Test def testPipe(): Unit = {
     val pipe = new Pipe1 | new Pipe2
     pipe.commandLine.contains("pipe1") shouldBe true
     pipe.commandLine.contains("input1") shouldBe true

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala

@@ -77,7 +77,7 @@ class CommandLineResourcesTest extends TestNGSuite with Matchers {
     val cmd1 = new CommandLineFunctionMock with CommandLineResources
     val cmd2 = new CommandLineFunctionMock with CommandLineResources
     val mainCmd = new CommandLineFunctionMock with CommandLineResources {
-      def combine(functions: List[CommandLineResources]) = combineResources(functions)
+      def combine(functions: List[CommandLineResources]): Unit = combineResources(functions)
     }
     mainCmd.combine(List(cmd1, cmd2))
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala

@@ -35,7 +35,7 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
   import MultiSampleQScriptTest._
 
   @Test
-  def testDefault: Unit = {
+  def testDefault(): Unit = {
 
     val script = MultiSampleQScriptTest(sample1 :: sample2 :: sample3 :: Nil)
     script.outputDir = new File("./").getAbsoluteFile
@@ -68,7 +68,7 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testTrio: Unit = {
+  def testTrio(): Unit = {
     val script = MultiSampleQScriptTest(child :: father :: mother :: Nil)
     script.init()
     script.biopetScript()
@@ -83,7 +83,7 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testGroups: Unit = {
+  def testGroups(): Unit = {
     val script = MultiSampleQScriptTest(sample1 :: sample2 :: sample3 :: Nil)
     script.init()
     script.biopetScript()
@@ -99,7 +99,7 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testOnlySamples: Unit = {
+  def testOnlySamples(): Unit = {
     val script = MultiSampleQScriptTest(sample1 :: sample2 :: sample3 :: Nil, List("sample1"))
     script.init()
     script.biopetScript()
@@ -108,7 +108,7 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testInvalidSampleName: Unit = {
+  def testInvalidSampleName(): Unit = {
     val script = MultiSampleQScriptTest(sample4 :: Nil)
     script.init()
     script.biopetScript()
@@ -210,13 +210,20 @@ object MultiSampleQScriptTest {
     )
   )
 
-  def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = {
+  def apply(configs: List[Map[String, Any]], only: List[String] = Nil): QScript with MultiSampleQScript {
+    def init(): Unit
+
+    def getLastLogMessage: String
+
+    def biopetScript(): Unit
+
+  } = {
     new QScript with MultiSampleQScript { qscript =>
 
       qSettings = new QSettings()
       qSettings.runName = "test"
 
-      override val onlySamples = only
+      override val onlySamples: List[String] = only
 
       var buffer = new ListBuffer[String]()