From dd6abc7efdcaa4a698ab1e15fcd8a8caf023a05d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 18:21:46 +0100
Subject: [PATCH] Fix "/" format errors
---
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 1bd5b1df7..46e2107dd 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -172,7 +172,7 @@ object Fastqc {
if (filename.endsWith(".gzip")) filename = filename.substring(0, filename.size - 5)
if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
- fastqcCommand.output = new File(outDir, "/" + filename + "_fastqc.zip")
+ fastqcCommand.output = new File(outDir, filename + "_fastqc.zip")
fastqcCommand.beforeGraph
fastqcCommand
}
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 e4cea2932..c83014c44 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
@@ -127,7 +127,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def biopetScript() {
if (!skipFlexiprep) {
- flexiprep.outputDir = new File(outputDir, "flexiprep" + File.separator)
+ flexiprep.outputDir = new File(outputDir, "flexiprep")
flexiprep.input_R1 = input_R1
flexiprep.input_R2 = input_R2
flexiprep.sampleId = this.sampleId
@@ -146,7 +146,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
var chunks: Map[File, (String, String)] = Map()
if (chunking) for (t <- 1 to numberChunks.getOrElse(1)) {
- val chunkDir = new File(outputDir, "chunks/" + t + "/")
+ val chunkDir = new File(outputDir, "chunks" + File.separator + t)
chunks += (chunkDir -> (removeGz(chunkDir + input_R1.getName),
if (paired) removeGz(chunkDir + input_R2.get.getName) else ""))
}
--
GitLab