Commit 50feeba1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added scala docs

parent 62b94624
......@@ -23,6 +23,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
/**
* Queue extension for the FastqSplitter
* @param root Parent object
*/
class FastqSplitter(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
......@@ -35,10 +39,20 @@ class FastqSplitter(val root: Configurable) extends BiopetJavaCommandLineFunctio
override val defaultVmem = "8G"
memoryLimit = Option(4.0)
/**
* Generate command to execute
* @return
*/
override def commandLine = super.commandLine + required("-I", input) + repeat("-o", output)
}
object FastqSplitter extends ToolCommand {
/**
* Arg for commandline program
* @param inputFile input fastq file
* @param outputFile output fastq files
*/
case class Args(inputFile: File = null, outputFile: List[File] = Nil) extends AbstractArgs
class OptParser extends AbstractOptParser {
......@@ -51,6 +65,8 @@ object FastqSplitter extends ToolCommand {
}
/**
* Program will split fastq file in multiple fastq files
*
* @param args the command line arguments
*/
def main(args: Array[String]): Unit = {
......
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