Commit 47b02b54 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed graph issue

parent 5d5c30c1
......@@ -177,26 +177,19 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
var fastq_R1_output: List[File] = Nil
var fastq_R2_output: List[File] = Nil
def removeGz(file: File): File = {
val absPath = file.getAbsolutePath
if (absPath.endsWith(".gz")) new File(absPath.substring(0, absPath.lastIndexOf(".gz")))
else if (absPath.endsWith(".gzip")) new File(absPath.substring(0, absPath.lastIndexOf(".gzip")))
else file
val chunks: Map[File, (File, Option[File])] = {
if (chunking) {
(for (t <- 1 to numberChunks.getOrElse(1)) yield {
val chunkDir = new File(outputDir, "chunks" + File.separator + t)
chunkDir -> (removeGz(new File(chunkDir, input_R1.getName)),
if (paired) Some(removeGz(new File(chunkDir, input_R2.get.getName))) else None)
chunkDir -> (new File(chunkDir, input_R1.getName),
if (paired) Some(new File(chunkDir, input_R2.get.getName)) else None)
} else if (skipFlexiprep) {
Map(outputDir -> (
extractIfNeeded(input_R1, flexiprep.outputDir),
if (paired) Some(extractIfNeeded(input_R2.get, outputDir)) else None)
} else Map(outputDir -> (flexiprep.fastqR1Qc, flexiprep.fastqR2Qc))
} else Map(outputDir -> (flexiprep.input_R1, flexiprep.input_R2))
if (chunking) {
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