Changes to conform to Scala syntax

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2015 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.core.{BiopetJavaCommandLineFunction, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+/**
+ * Wrapper for the Cnmops command line tool.
+ * Written based on Cnmops version v2.2.1.
+ */
+class Cnmops(val root: Configurable) extends BiopetJavaCommandLineFunction {
+  javaMainClass = getClass.getName
+
+  /** input file */
+  @Input(doc = "Input file BAM", required = true)
+  var input: List[File] = List()
+
+  /** output files, computed automatically from output directory */
+
+  @Output(doc = "Output CNV file")
+  lazy val output_cnv: File = {
+    if (output_dir == null)
+      throw new RuntimeException("Unexpected error when trying to set cn.MOPS CNV output")
+    new File(output_dir,  "cnv.txt")
+  }
+  @Output(doc = "Output CNR file")
+  lazy val output_cnr: File = {
+    if (output_dir == null)
+      throw new RuntimeException("Unexpected error when trying to set cn.MOPS CNR output")
+    new File(output_dir,  "cnr.txt")
+  }
+
+  /** write all output files to this directory [./] */
+  var output_dir: String = _
+
+  override def beforeGraph = {
+    super.beforeGraph
+    require(!output_dir.isEmpty, "Outputdir for cn.MOPS should not be empty")
+    require(input.length > 1, "Please supply at least 2 BAM files for cn.MOPS")
+  }
+
+  override val versionRegex = """Cnmops v(.*)""".r
+  override def versionCommand = executable
+
+  def cmdLine = {
+    required(executable) +
+      required("--output-dir", output_dir) +
+      required(input)
+  }
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.Input
+
+/**
+ * Created by wyleung on 17-2-15.
+ */
+trait RscriptCommandLineFunction  extends BiopetCommandLineFunction{
+  @Input(doc = "R script", required = false)
+  var script: File = _
+  protected var scriptName: String = _
+
+  executable = config("exe", default = "Rscript", submodule = "R")
+
+
+  /**
+   * Set the Rscript to run
+   *
+   * @param filename RScript file location
+   */
+  def setScript(filename: File) = {
+
+
+  }
+
+  def setScript(filename: File, subpackage: String) = {
+
+
+  }
+
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala

@@ -10,7 +10,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 import scala.collection.JavaConverters._
 import scala.collection.mutable
-import scala.collection.immutable.{ Map }
+import scala.collection.immutable.Map
 import scala.io.Source
 import scala.language.postfixOps
 
@@ -32,20 +32,20 @@ class Seqstat(val root: Configurable) extends BiopetJavaCommandLineFunction {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input FASTQ", shortName = "input", required = true)
-  var input: File = _
+  var input: File = null
 
   @Output(doc = "Output JSON", shortName = "output", required = true)
-  var output: File = _
+  var output: File = null
 
   override val defaultVmem = "4G"
   memoryLimit = Option(3.0)
 
   override def commandLine = super.commandLine + required("-i", input) + " > " + required(output)
 
-  def getSummary: Json = {
+  def summary: Json = {
     val json = Parse.parseOption(Source.fromFile(output).mkString)
-    if (json.isEmpty) return jNull
-    else return json.get.fieldOrEmptyObject("stats")
+    if (json.isEmpty) jNull
+    else json.get.fieldOrEmptyObject("stats")
   }
 }
 
@@ -61,7 +61,7 @@ object Seqstat extends ToolCommand {
     val seqstat = new Seqstat(root)
     seqstat.input = input
     seqstat.output = output
-    return seqstat
+    seqstat
   }
 
   def apply(root: Configurable, fastqfile: File, outDir: String): Seqstat = {
@@ -69,7 +69,7 @@ object Seqstat extends ToolCommand {
     val ext = fastqfile.getName.substring(fastqfile.getName.lastIndexOf("."))
     seqstat.input = fastqfile
     seqstat.output = new File(outDir + fastqfile.getName.substring(0, fastqfile.getName.lastIndexOf(".")) + ".seqstats.json")
-    return seqstat
+    seqstat
   }
 
   def mergeSummaries(jsons: List[Json]): Json = {
@@ -101,7 +101,7 @@ object Seqstat extends ToolCommand {
       val reads = json.fieldOrEmptyObject("reads")
       addJson(reads, readsTotal)
     }
-    return ("bases" := (
+    ("bases" := (
       ("num_n" := basesTotal("num_n")) ->:
       ("num_total" := basesTotal("num_total")) ->:
       ("num_qual_gte" := (
@@ -254,7 +254,7 @@ object Seqstat extends ToolCommand {
     }
 
     // implicit conversion to Int using foldLeft(0)
-    val avgQual: Int = (readQual.foldLeft(0)(_ + _) / readQual.length)
+    val avgQual: Int = (readQual.sum / readQual.length)
     if (readStats.qual.length <= avgQual) {
       readStats.qual ++= mutable.ArrayBuffer.fill(avgQual - readStats.qual.length + 1)(0)
     }

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala

@@ -149,25 +149,25 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
   }
 
   def seqstatSummary(): Option[Json] = {
-    val R1_chunks = for ((key, value) <- chunks) yield value.seqstatR1.getSummary
+    val R1_chunks = for ((key, value) <- chunks) yield value.seqstatR1.summary
     val R1: Json = Seqstat.mergeSummaries(R1_chunks.toList)
 
     val R2: Option[Json] = if (!flexiprep.paired) None
-    else if (chunks.size == 1) Option(chunks.head._2.seqstatR2.getSummary)
+    else if (chunks.size == 1) Option(chunks.head._2.seqstatR2.summary)
     else {
-      val s = for ((key, value) <- chunks) yield value.seqstatR2.getSummary
+      val s = for ((key, value) <- chunks) yield value.seqstatR2.summary
       Option(Seqstat.mergeSummaries(s.toList))
     }
     val R1_proc: Option[Json] = if (flexiprep.skipClip && flexiprep.skipTrim) None
-    else if (chunks.size == 1) Option(chunks.head._2.seqstatR1after.getSummary)
+    else if (chunks.size == 1) Option(chunks.head._2.seqstatR1after.summary)
     else {
-      val s = for ((key, value) <- chunks) yield value.seqstatR1after.getSummary
+      val s = for ((key, value) <- chunks) yield value.seqstatR1after.summary
       Option(Seqstat.mergeSummaries(s.toList))
     }
     val R2_proc: Option[Json] = if (!flexiprep.paired || (flexiprep.skipClip && flexiprep.skipTrim)) None
-    else if (chunks.size == 1) Option(chunks.head._2.seqstatR2after.getSummary)
+    else if (chunks.size == 1) Option(chunks.head._2.seqstatR2after.summary)
     else {
-      val s = for ((key, value) <- chunks) yield value.seqstatR2after.getSummary
+      val s = for ((key, value) <- chunks) yield value.seqstatR2after.summary
       Option(Seqstat.mergeSummaries(s.toList))
     }
     return Option(("R1_raw" := R1) ->: