From 7b8a06ed5722e3aa796bc426466b613e5b25f22a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 14 Feb 2015 15:02:58 +0100
Subject: [PATCH] Fix outputDirs
---
.../nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
index e76acd863..8c1f543bf 100644
--- a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
@@ -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()
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 8dbf2f035..e6e483ab4 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -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)
--
GitLab