Commit e294fd51 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Move init jobs for flexiprep out of chunks

parent d26a67ab
......@@ -124,7 +124,15 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var fastq_R1: File = input_R1
var fastq_R2: File = if (paired) input_R2 else ""
val flexiprep = new Flexiprep(this)
flexiprep.outputDir = outputDir + "flexiprep/"
if (!skipFlexiprep) {
flexiprep.outputDir = outputDir + "flexiprep/"
flexiprep.input_R1 = fastq_R1
if (paired) flexiprep.input_R2 = fastq_R2
flexiprep.sampleName = this.RGSM
flexiprep.libraryName = this.RGLB
flexiprep.init
flexiprep.runInitialJobs
}
var bamFiles: List[File] = Nil
var fastq_R1_output: List[File] = Nil
var fastq_R2_output: List[File] = Nil
......@@ -166,13 +174,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var deps: List[File] = Nil
val chunkDir = if (chunking) outputDir + chunk + "/" else outputDir
if (!skipFlexiprep) {
flexiprep.input_R1 = fastq_R1
if (paired) flexiprep.input_R2 = fastq_R2
flexiprep.sampleName = this.RGSM
flexiprep.libraryName = this.RGLB
flexiprep.init
flexiprep.runInitialJobs
//flexiprep.biopetScript
val flexiout = flexiprep.runTrimClip(R1, R2, chunkDir + "flexiprep/", chunk)
logger.debug(chunk + " - " + flexiout)
R1 = flexiout._1
......
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