Commit 18e080e1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Moved Flexiprep val to root op mapping class

parent 89121481
......@@ -75,6 +75,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var RGPI: Int = _
var paired: Boolean = false
val flexiprep = new Flexiprep(this)
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
......@@ -123,7 +125,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def biopetScript() {
var fastq_R1: File = input_R1
var fastq_R2: File = if (paired) input_R2 else ""
val flexiprep = new Flexiprep(this)
if (!skipFlexiprep) {
flexiprep.outputDir = outputDir + "flexiprep/"
flexiprep.input_R1 = fastq_R1
......
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