Commit 7b8a06ed authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix outputDirs

parent 1926c8f8
......@@ -46,7 +46,7 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
object Bam2Wig extends PipelineCommand {
def apply(root: Configurable, bamFile: File): Bam2Wig = {
val bamToBigWig = new Bam2Wig(root)
bamToBigWig.outputDir = bamFile.getParent
bamToBigWig.outputDir = bamFile.getParentFile
bamToBigWig.bamFile = bamFile
bamToBigWig.init()
bamToBigWig.biopetScript()
......
......@@ -186,7 +186,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
fastq_R2_output :+= R2
}
val outputBam = new File(chunkDir + outputName + ".bam")
val outputBam = new File(chunkDir, outputName + ".bam")
bamFiles :+= outputBam
aligner match {
case "bwa" => addBwaMem(R1, R2, outputBam, deps)
......@@ -198,7 +198,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
case _ => throw new IllegalStateException("Option Aligner: '" + aligner + "' is not valid")
}
if (config("chunk_metrics", default = false))
addAll(BamMetrics(this, outputBam, chunkDir + "metrics/").functions)
addAll(BamMetrics(this, outputBam, new File(chunkDir, "metrics")).functions)
}
if (!skipFlexiprep) {
flexiprep.runFinalize(fastq_R1_output, fastq_R2_output)
......
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