Commit 1ca59443 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change chunk directory

parent c36fb267
......@@ -144,11 +144,11 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
var chunks: Map[String, (String, String)] = Map()
if (chunking) for (t <- 1 to numberChunks.getOrElse(1)) {
chunks += ("chunk_" + t -> (removeGz(outputDir + "chunk_" + t + "/" + fastq_R1.getName),
if (paired) removeGz(outputDir + "chunk_" + t + "/" + fastq_R2.getName) else ""))
}
else chunks += ("flexiprep" -> (flexiprep.extractIfNeeded(fastq_R1, flexiprep.outputDir),
flexiprep.extractIfNeeded(fastq_R2, flexiprep.outputDir)))
val chunkDir = "chunks/" + t + "/"
chunks += (chunkDir -> (removeGz(chunkDir + fastq_R1.getName),
if (paired) removeGz(chunkDir + fastq_R2.getName) else ""))
} else chunks += ("flexiprep/" -> (flexiprep.extractIfNeeded(fastq_R1, flexiprep.outputDir),
flexiprep.extractIfNeeded(fastq_R2, flexiprep.outputDir)))
if (chunking) {
val fastSplitter_R1 = new FastqSplitter(this)
......@@ -172,7 +172,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var R1 = fastqfile._1
var R2 = fastqfile._2
var deps: List[File] = Nil
val chunkDir = if (chunking) outputDir + chunk + "/" else outputDir
val chunkDir = if (chunking) outputDir + chunk else outputDir
if (!skipFlexiprep) {
val flexiout = flexiprep.runTrimClip(R1, R2, chunkDir + "flexiprep/", chunk)
logger.debug(chunk + " - " + flexiout)
......
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