Commit 4e925feb authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed file location when not chunking

parent 9be7a784
......@@ -137,7 +137,8 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
if (chunking) for (t <- 1 to numberChunks) {
chunks += ("chunk_" + t -> (removeGz(outputDir + "chunk_" + t + "/" + fastq_R1.getName),
if (paired) removeGz(outputDir + "chunk_" + t + "/" + fastq_R2.getName) else ""))
} else chunks += (flexiprep.outputDir -> (fastq_R1,fastq_R2))
} else chunks += ("flexiprep" -> (flexiprep.extractIfNeeded(fastq_R1, flexiprep.outputDir),
flexiprep.extractIfNeeded(fastq_R2, flexiprep.outputDir)))
if (chunking) {
val fastSplitter_R1 = new FastqSplitter(this)
......@@ -163,6 +164,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
if (!skipFlexiprep) {
flexiprep.input_R1 = fastq_R1
if (paired) flexiprep.input_R2 = fastq_R2
flexiprep.skipSummary = true
flexiprep.init
flexiprep.runInitialJobs
//flexiprep.biopetScript
......@@ -173,7 +175,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
fastq_R1_output :+= R1
fastq_R2_output :+= R2
}
val chunkDir = if (chunk.isEmpty) outputDir else outputDir + chunk + "/"
val chunkDir = if (chunking) outputDir + chunk + "/" else outputDir
if (aligner == "bwa") {
val bwaCommand = new Bwa(this)
bwaCommand.R1 = R1
......
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