Commit 28d55721 authored by bow's avatar bow
Browse files

Refactor FastQC outputDir and dataFile to separate methods

parent 46c811a1
......@@ -34,6 +34,14 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
*/
class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) {
/** Default FastQC output directory containing actual results */
// this is a def instead of a val since the value depends on the variable `output`, which is null on class creation
def outputDir: File = new File(output.getAbsolutePath.stripSuffix(".zip"))
/** Default FastQC output data file */
// this is a def instead of a val since the value depends on the variable `output`, which is null on class creation
def dataFile: File = new File(outputDir, "fastqc_data.txt")
/**
* FastQC QC modules.
*
......@@ -43,10 +51,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
*/
@throws(classOf[FileNotFoundException])
@throws(classOf[IllegalStateException])
protected def qcModules: Map[String, Array[String]] = {
val outputDir = output.getAbsolutePath.stripSuffix(".zip")
val dataFile = new File(outputDir, "fastqc_data.txt")
def qcModules: Map[String, Array[String]] = {
val fqModules = Source.fromFile(dataFile)
// drop all the characters before the first module delimiter (i.e. '>>')
......@@ -128,7 +133,6 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
/** Summary of the FastQC run, stored in a [[Json]] object */
def summary: Json = {
val outputDir: String = output.getAbsolutePath.stripSuffix(".zip")
val outputMap =
Map("plot_duplication_levels" -> "Images/duplication_levels.png",
"plot_kmer_profiles" -> "Images/kmer_profiles.png",
......
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