Commit c2284b8b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed chunking output dirs

parent a827c3b4
...@@ -143,38 +143,33 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript { ...@@ -143,38 +143,33 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
} }
var chunks: Map[String, (String, String)] = Map() var chunks: Map[String, (String, String)] = Map()
if (chunking) for (t <- 1 to numberChunks.getOrElse(1)) { if (chunking) for (t <- 1 to numberChunks.getOrElse(1)) {
val chunkDir = "chunks/" + t + "/" val chunkDir = outputDir + "chunks/" + t + "/"
chunks += (chunkDir -> (removeGz(chunkDir + fastq_R1.getName), chunks += (chunkDir -> (removeGz(chunkDir + fastq_R1.getName),
if (paired) removeGz(chunkDir + fastq_R2.getName) else "")) if (paired) removeGz(chunkDir + fastq_R2.getName) else ""))
} else chunks += ("flexiprep/" -> (flexiprep.extractIfNeeded(fastq_R1, flexiprep.outputDir), } else chunks += (outputDir -> (flexiprep.extractIfNeeded(fastq_R1, flexiprep.outputDir),
flexiprep.extractIfNeeded(fastq_R2, flexiprep.outputDir))) flexiprep.extractIfNeeded(fastq_R2, flexiprep.outputDir)))
if (chunking) { if (chunking) {
val fastSplitter_R1 = new FastqSplitter(this) val fastSplitter_R1 = new FastqSplitter(this)
fastSplitter_R1.input = fastq_R1 fastSplitter_R1.input = fastq_R1
fastSplitter_R1.memoryLimit = 4 for ((chunkDir, fastqfile) <- chunks) fastSplitter_R1.output :+= fastqfile._1
fastSplitter_R1.jobResourceRequests :+= "h_vmem=8G"
for ((chunk, fastqfile) <- chunks) fastSplitter_R1.output :+= fastqfile._1
add(fastSplitter_R1) add(fastSplitter_R1)
if (paired) { if (paired) {
val fastSplitter_R2 = new FastqSplitter(this) val fastSplitter_R2 = new FastqSplitter(this)
fastSplitter_R2.input = fastq_R2 fastSplitter_R2.input = fastq_R2
fastSplitter_R2.memoryLimit = 4 for ((chunkDir, fastqfile) <- chunks) fastSplitter_R2.output :+= fastqfile._2
fastSplitter_R2.jobResourceRequests :+= "h_vmem=8G"
for ((chunk, fastqfile) <- chunks) fastSplitter_R2.output :+= fastqfile._2
add(fastSplitter_R2) add(fastSplitter_R2)
} }
} }
for ((chunk, fastqfile) <- chunks) { for ((chunkDir, fastqfile) <- chunks) {
var R1 = fastqfile._1 var R1 = fastqfile._1
var R2 = fastqfile._2 var R2 = fastqfile._2
var deps: List[File] = Nil var deps: List[File] = Nil
val chunkDir = if (chunking) outputDir + chunk else outputDir
if (!skipFlexiprep) { if (!skipFlexiprep) {
val flexiout = flexiprep.runTrimClip(R1, R2, chunkDir + "flexiprep/", chunk) val flexiout = flexiprep.runTrimClip(R1, R2, chunkDir + "flexiprep/", chunkDir)
logger.debug(chunk + " - " + flexiout) logger.debug(chunkDir + " - " + flexiout)
R1 = flexiout._1 R1 = flexiout._1
if (paired) R2 = flexiout._2 if (paired) R2 = flexiout._2
deps = flexiout._3 deps = flexiout._3
......
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