Inspection round Biopet Extensions

biopet-extensions/pom.xml

@@ -33,12 +33,6 @@
             <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
-        <dependency>
-            <groupId>org.testng</groupId>
-            <artifactId>testng</artifactId>
-            <version>6.8</version>
-            <scope>test</scope>
-        </dependency>
     </dependencies>
 
 </project>
\ No newline at end of file

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala

@@ -40,7 +40,7 @@ class Awk(val parent: Configurable) extends BiopetCommandLineFunction with Versi
 
   var command: String = _
 
-  def cmdLine =
+  def cmdLine: String =
     executable +
       required(command) +
       (if (inputAsStdin) "" else required(input)) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala

@@ -35,7 +35,7 @@ class Cat(val parent: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "cat")
 
   /** return commandline to execute */
-  def cmdLine =
+  def cmdLine: String =
     required(executable) +
       (if (inputAsStdin) "" else repeat(input)) +
       (if (outputAsStdout) "" else (if (appending) " >> " else " > ") + required(output))

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cp.scala

@@ -19,7 +19,7 @@ class Cp(val parent: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "cp")
 
   /** Returns command to execute */
-  def cmdLine =
+  def cmdLine: String =
     required(executable) +
       required(source) +
       required(target)

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala

@@ -16,10 +16,12 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
+import scala.util.matching.Regex
+
 /**
   * Wrapper for the cufflinks command line tool.
   * Written based on cufflinks version v2.2.1 (md5: 07c831c4f8b4e161882731ea5694ff80)
@@ -37,7 +39,7 @@ class Cufflinks(val parent: Configurable) extends BiopetCommandLineFunction with
 
   /** input file */
   @Input(doc = "Input file (SAM or BAM)", required = true)
-  var input: File = null
+  var input: File = _
 
   /** output files, computed automatically from output directory */
   @Output(doc = "Output GTF file")
@@ -187,11 +189,11 @@ class Cufflinks(val parent: Configurable) extends BiopetCommandLineFunction with
   /** do not contact server to check for update availability [FALSE] */
   var noUpdateCheck: Boolean = config("no_update_check", default = false)
 
-  def versionRegex = """cufflinks v(.*)""".r
-  def versionCommand = executable
+  def versionRegex: Regex = """cufflinks v(.*)""".r
+  def versionCommand: String = executable
   override def versionExitcode = List(0, 1)
 
-  def cmdLine =
+  def cmdLine: String =
     required(executable) +
       required("--output-dir", outputDir) +
       optional("--num-threads", threads) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala

@@ -16,10 +16,12 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Output
 
+import scala.util.matching.Regex
+
 /**
   * Created by pjvan_thof on 8/11/15.
   */
@@ -30,8 +32,8 @@ class Curl(val parent: Configurable) extends BiopetCommandLineFunction with Vers
   var url: String = _
 
   executable = config("exe", default = "curl")
-  def versionCommand = executable + " --version"
-  def versionRegex = """curl (\w+\.\w+\.\w+) .*""".r
+  def versionCommand: String = executable + " --version"
+  def versionRegex: Regex = """curl (\w+\.\w+\.\w+) .*""".r
 
   def cmdLine: String =
     required(executable) + required(url) + (if (outputAsStdout) "" else " > " + required(output))

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

@@ -44,8 +44,8 @@ class Cutadapt(val parent: Configurable)
   var statsOutput: File = _
 
   executable = config("exe", default = "cutadapt")
-  def versionCommand = executable + " --version"
-  def versionRegex = """(.*)""".r
+  def versionCommand: String = executable + " --version"
+  def versionRegex: Regex = """(.*)""".r
 
   /** Name of the key containing clipped adapters information in the summary stats. */
   def adaptersStatsName = "adapters"
@@ -112,7 +112,7 @@ class Cutadapt(val parent: Configurable)
   var untrimmedPairedOutput: Option[File] = config("untrimmed_paired_output")
 
   /** return commandline to execute */
-  def cmdLine =
+  def cmdLine: String =
     required(executable) +
       // Options that influence how the adapters are found
       repeat("-a", adapter) +
@@ -187,10 +187,9 @@ class Cutadapt(val parent: Configurable)
         // identify the adapter name and count
         for (line <- adapter.split("\n")) {
           line match {
-            case adapterR(adapter, count) => {
+            case adapterR(adapter, count) =>
               adapterName = adapter
               adapterCount = count.toInt
-            }
             case _ =>
           }
         }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

@@ -21,6 +21,8 @@ import nl.lumc.sasc.biopet.utils.SemanticVersion
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
+import scala.util.matching.Regex
+
 /**
   * Extension for fastqc
   * Based on version 0.10.1 and 0.11.2
@@ -34,10 +36,10 @@ class Fastqc(val parent: Configurable) extends BiopetCommandLineFunction with Ve
   var adapters: Option[File] = None
 
   @Input(doc = "Fastq file", shortName = "FQ")
-  var fastqfile: File = null
+  var fastqfile: File = _
 
   @Output(doc = "Output", shortName = "out", required = true)
-  var output: File = null
+  var output: File = _
 
   executable = config("exe", default = "fastqc")
   var javaExe: String = config("exe", default = "java", namespace = "java", freeVar = false)
@@ -47,8 +49,8 @@ class Fastqc(val parent: Configurable) extends BiopetCommandLineFunction with Ve
   var nogroup: Boolean = config("nogroup", default = false)
   var extract: Boolean = config("extract", default = true)
 
-  def versionRegex = """FastQC (.*)""".r
-  def versionCommand = executable + " --version"
+  def versionRegex: Regex = """FastQC (.*)""".r
+  def versionCommand: String = executable + " --version"
   override def defaultThreads = 4
 
   /** Sets contaminants and adapters when not yet set */
@@ -86,7 +88,7 @@ class Fastqc(val parent: Configurable) extends BiopetCommandLineFunction with Ve
   }
 
   /** return commandline to execute */
-  def cmdLine =
+  def cmdLine: String =
     required(executable) +
       optional("--java", javaExe) +
       optional("--threads", threads) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala

@@ -92,7 +92,7 @@ class Flash(val parent: Configurable) extends BiopetCommandLineFunction with Ver
     _outputHistogram = outputHistogram
   }
 
-  def cmdLine =
+  def cmdLine: String =
     executable +
       optional("-m", minOverlap) +
       optional("-M", maxOverlap) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala

@@ -17,9 +17,11 @@ package nl.lumc.sasc.biopet.extensions
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction, Reference}
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
 import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
+import scala.util.matching.Regex
+
 /**
   * Extension for freebayes
   *
@@ -37,7 +39,7 @@ class Freebayes(val parent: Configurable)
   var reference: File = _
 
   @Output(required = true)
-  var outputVcf: File = null
+  var outputVcf: File = _
 
   @Input(required = false)
   var bamList: Option[File] = config("bam_list")
@@ -129,15 +131,15 @@ class Freebayes(val parent: Configurable)
   var haplotypeLength: Option[Int] = config("haplotype_length")
 
   executable = config("exe", default = "freebayes")
-  def versionRegex = """version:  (.*)""".r
-  def versionCommand = executable + " --version"
+  def versionRegex: Regex = """version:  (.*)""".r
+  def versionCommand: String = executable + " --version"
 
   override def beforeGraph(): Unit = {
     super.beforeGraph()
     reference = referenceFasta()
   }
 
-  def cmdLine =
+  def cmdLine: String =
     executable +
       required("--fasta-reference", reference) +
       repeat("--bam", bamfiles) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala

@@ -35,7 +35,7 @@ class GffRead(val parent: Configurable) extends BiopetCommandLineFunction {
 
   var T: Boolean = config("T", default = false, freeVar = false)
 
-  def cmdLine =
+  def cmdLine: String =
     executable +
       (if (inputAsStdin) "" else required(input)) +
       (if (outputAsStdout) "" else required("-o", output)) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala

@@ -32,14 +32,14 @@ class Grep(val parent: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "grep")
 
-  var grepFor: String = null
+  var grepFor: String = _
 
   var invertMatch: Boolean = false
   var regex: Boolean = false
   var perlRegexp: Boolean = false
 
   /** return commandline to execute */
-  def cmdLine =
+  def cmdLine: String =
     required(executable) +
       conditional(invertMatch, "-v") +
       conditional(regex, "-e") +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala

@@ -41,7 +41,7 @@ class GtfToGenePred(val parent: Configurable) extends BiopetCommandLineFunction
   var simple: Boolean = config("simple", default = false)
   var geneNameAsName2: Boolean = config("gene _name_as_name2", default = false)
 
-  def cmdLine =
+  def cmdLine: String =
     executable +
       conditional(genePredExt, "-genePredExt") +
       conditional(allErrors, "-allErrors") +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala

@@ -16,10 +16,12 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
+import scala.util.matching.Regex
+
 class Gzip(val parent: Configurable) extends BiopetCommandLineFunction with Version {
   @Input(doc = "Input file", required = true)
   var input: List[File] = Nil
@@ -29,10 +31,10 @@ class Gzip(val parent: Configurable) extends BiopetCommandLineFunction with Vers
 
   executable = config("exe", default = "gzip", freeVar = false)
 
-  def versionRegex = """gzip (.*)""".r
-  def versionCommand = executable + " --version"
+  def versionRegex: Regex = """gzip (.*)""".r
+  def versionCommand: String = executable + " --version"
 
-  def cmdLine =
+  def cmdLine: String =
     required(executable) + " -c " +
       (if (inputAsStdin) "" else repeat(input)) +
       (if (outputAsStdout) "" else " > " + required(output))

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala

@@ -16,10 +16,12 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
+import scala.util.matching.Regex
+
 /**
   * Wrapper for the htseq-count command line tool
   * Written based on htseq-count version 0.6.1p1
@@ -31,15 +33,15 @@ class HtseqCount(val parent: Configurable) extends BiopetCommandLineFunction wit
 
   /** input file */
   @Input(doc = "Input alignment file", required = true)
-  var inputAlignment: File = null
+  var inputAlignment: File = _
 
   /** input GFF / GTF annotation file */
   @Input(doc = "Input GFF / GTF annotation file", required = true)
-  var inputAnnotation: File = null
+  var inputAnnotation: File = _
 
   /** output file */
   @Output(doc = "Output count file", required = true)
-  var output: File = null
+  var output: File = _
 
   /** type of input alignment */
   var format: Option[String] = config("format")
@@ -69,10 +71,10 @@ class HtseqCount(val parent: Configurable) extends BiopetCommandLineFunction wit
   /** suppress progress report */
   var quiet: Boolean = config("quiet", default = false)
 
-  def versionRegex = """.*, version (.*)\.""".r
-  def versionCommand = executable + " --help"
+  def versionRegex: Regex = """.*, version (.*)\.""".r
+  def versionCommand: String = executable + " --help"
 
-  def cmdLine = {
+  def cmdLine: String = {
     required(executable) +
       optional("--format", format) +
       optional("--order", order) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala

@@ -33,7 +33,7 @@ class Pbzip2(val parent: Configurable) extends BiopetCommandLineFunction {
   var decomrpess = true
   var memory: Option[Int] = config("memory")
 
-  override def defaultCoreMemory = memory.getOrElse(1000).toDouble / 1000
+  override def defaultCoreMemory: Double = memory.getOrElse(1000).toDouble / 1000
   override def defaultThreads = 2
 
   override def beforeCmd() {
@@ -41,7 +41,7 @@ class Pbzip2(val parent: Configurable) extends BiopetCommandLineFunction {
   }
 
   /** return commandline to execute */
-  def cmdLine =
+  def cmdLine: String =
     required(executable) +
       conditional(decomrpess, "-d") +
       conditional(!decomrpess, "-z") +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala

@@ -21,6 +21,8 @@ import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline._
 
+import scala.util.matching.Regex
+
 /**
   * Created by wyleung on 8-1-16.
   */
@@ -43,8 +45,8 @@ class Pysvtools(val parent: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "vcf_merge_sv_events")
 
-  def versionRegex = """PySVtools (.*)""".r
-  def versionCommand = executable + " --version"
+  def versionRegex: Regex = """PySVtools (.*)""".r
+  def versionCommand: String = executable + " --version"
   override def defaultThreads = 2
 
   override def beforeGraph(): Unit = {
@@ -61,7 +63,7 @@ class Pysvtools(val parent: Configurable) extends BiopetCommandLineFunction {
   }
 
   /** return commandline to execute */
-  def cmdLine =
+  def cmdLine: String =
     required(executable) +
       repeat("-c", exclusionRegions) +
       optional("-f", flanking) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala

@@ -16,10 +16,11 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
 
+import scala.util.matching.Regex
 import scalaz.std.boolean.option
 
 /**
@@ -29,8 +30,8 @@ import scalaz.std.boolean.option
 class Raxml(val parent: Configurable) extends BiopetCommandLineFunction with Version {
 
   override def defaultThreads = 1
-  def versionCommand = executable + " -v"
-  def versionRegex = """.*version ([\w\.]*) .*""".r
+  def versionCommand: String = executable + " -v"
+  def versionRegex: Regex = """.*version ([\w\.]*) .*""".r
 
   @Input(doc = "Input phy/fasta file", required = true)
   var input: File = _
@@ -54,7 +55,7 @@ class Raxml(val parent: Configurable) extends BiopetCommandLineFunction with Ver
   var f: String = "d"
 
   @Argument(doc = "Output directory", required = true)
-  var w: File = null
+  var w: File = _
 
   @Input(required = false)
   var t: Option[File] = _
@@ -91,19 +92,19 @@ class Raxml(val parent: Configurable) extends BiopetCommandLineFunction with Ver
   }
 
   /** Returns bestTree file */
-  def getBestTreeFile = option(f == "d" && b.isEmpty, new File(w, "RAxML_bestTree." + n))
+  def getBestTreeFile: Option[File] = option(f == "d" && b.isEmpty, new File(w, "RAxML_bestTree." + n))
 
   /** Returns bootstrap file */
-  def getBootstrapFile = option(f == "d" && b.isDefined, new File(w, "RAxML_bootstrap." + n))
+  def getBootstrapFile: Option[File] = option(f == "d" && b.isDefined, new File(w, "RAxML_bootstrap." + n))
 
   /** Returns bipartitions file */
-  def getBipartitionsFile = option(f == "b", new File(w, "RAxML_bipartitions." + n))
+  def getBipartitionsFile: Option[File] = option(f == "b", new File(w, "RAxML_bipartitions." + n))
 
   /** Returns info file */
   def getInfoFile = new File(w, "RAxML_info." + n)
 
   /** return commandline to execute */
-  def cmdLine =
+  def cmdLine: String =
     required(executable) +
       required("-m", m) +
       required("-s", input) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

@@ -34,7 +34,7 @@ class RunGubbins(val parent: Configurable) extends BiopetCommandLineFunction {
   var fastafile: File = _
 
   @Argument(required = true)
-  var outputDirectory: File = null
+  var outputDirectory: File = _
 
   executable = config("exe", default = "run_gubbins.py")
   var outgroup: Option[String] = config("outgroup")
@@ -72,7 +72,7 @@ class RunGubbins(val parent: Configurable) extends BiopetCommandLineFunction {
   }
 
   /** Return command to execute */
-  def cmdLine =
+  def cmdLine: String =
     required("cd", outputDirectory) + " && " + required(executable) +
       optional("--outgroup", outgroup) +
       optional("--starting_tree", startingTree) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala

@@ -42,7 +42,7 @@ class Sed(val parent: Configurable) extends BiopetCommandLineFunction with Versi
 
   var expressions: List[String] = Nil
 
-  def cmdLine =
+  def cmdLine: String =
     executable +
       repeat("-e", expressions) +
       (if (inputAsStdin) "" else required(inputFile)) +