Commit c378965a authored by bow's avatar bow
Browse files

Style update for FastQC wrapper and object in Flexiprep

parent 0055d58e
......@@ -16,13 +16,14 @@
package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import java.io.{ File, FileNotFoundException }
import scala.io.Source
import argonaut._, Argonaut._
import scalaz._, Scalaz._
import nl.lumc.sasc.biopet.core.config.Configurable
class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) {
def getDataBlock(name: String): Array[String] = { // Based on Fastqc v0.10.1
val outputDir = output.getAbsolutePath.stripSuffix(".zip")
......@@ -95,6 +96,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
}
object Fastqc {
def apply(root: Configurable, fastqfile: File, outDir: String): Fastqc = {
val fastqcCommand = new Fastqc(root)
fastqcCommand.fastqfile = fastqfile
......@@ -105,6 +107,6 @@ object Fastqc {
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
fastqcCommand.output = new File(outDir + "/" + filename + "_fastqc.zip")
fastqcCommand.afterGraph
return fastqcCommand
fastqcCommand
}
}
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