Commit a0e16b2f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix on outputdir for flexiprep

parent 7c1fa255
......@@ -155,6 +155,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
for ((chunk, fastqfile) <- chunks) {
var R1 = fastqfile._1
var R2 = fastqfile._2
val chunkDir = if (chunking) outputDir + chunk + "/" else outputDir
if (!skipFlexiprep) {
flexiprep.input_R1 = fastq_R1
if (paired) flexiprep.input_R2 = fastq_R2
......@@ -162,14 +163,14 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
flexiprep.init
flexiprep.runInitialJobs
//flexiprep.biopetScript
val flexiout = flexiprep.runTrimClip(R1, R2, outputDir + chunk, chunk)
val flexiout = flexiprep.runTrimClip(R1, R2, chunkDir + "flexiprep/", chunk)
logger.debug(chunk + " - " + flexiout)
R1 = flexiout._1
if (paired) R2 = flexiout._2
fastq_R1_output :+= R1
fastq_R2_output :+= R2
}
val chunkDir = if (chunking) outputDir + chunk + "/" else outputDir
if (aligner == "bwa") {
val bwaCommand = new Bwa(this)
bwaCommand.R1 = R1
......
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