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Commit a2ebfada authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix outputDir for flexiprep

parent 21b032c9
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @ a2ebfada
......@@ -123,6 +123,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
var fastq_R1: File = input_R1
var fastq_R2: File = if (paired) input_R2 else ""
val flexiprep = new Flexiprep(this)
flexiprep.outputDir = outputDir + "flexiprep/"
var bamFiles:List[File] = Nil
var fastq_R1_output: List[File] = Nil
var fastq_R2_output: List[File] = Nil
......@@ -136,7 +137,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
if (chunking) for (t <- 1 to numberChunks) {
chunks += ("chunk_" + t -> (removeGz(outputDir + "chunk_" + t + "/" + fastq_R1.getName),
if (paired) removeGz(outputDir + "chunk_" + t + "/" + fastq_R2.getName) else ""))
} else chunks += ("" -> (fastq_R1,fastq_R2))
} else chunks += (flexiprep.outputDir -> (fastq_R1,fastq_R2))
if (chunking) {
val fastSplitter_R1 = new FastqSplitter(this)
......@@ -162,7 +163,6 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
if (!skipFlexiprep) {
flexiprep.input_R1 = fastq_R1
if (paired) flexiprep.input_R2 = fastq_R2
flexiprep.outputDir = outputDir + "flexiprep/"
flexiprep.init
flexiprep.runInitialJobs
//flexiprep.biopetScript
......
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