Commit bc930d51 authored by Peter van 't Hof's avatar Peter van 't Hof

Make centrifuge usable output method

parent d36878da
......@@ -94,18 +94,21 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
if (!skipFlexiprep) {
val flexiprep = new Flexiprep(this)
flexiprep.inputR1 = read1
flexiprep.inputR2 = read2
flexiprep.sampleId = if (sampleId.isEmpty) Some("noSampleName") else sampleId
flexiprep.libId = if (libId.isEmpty) Some("noLibName") else libId
flexiprep.outputDir = new File(outputDir, "flexiprep")
(flexiprep.fastqR1Qc, flexiprep.fastqR2Qc)
} else (read1, read2) { f =>
f.inputR1 = read1
f.inputR2 = read2
f.sampleId = Some(sampleId.getOrElse("noSampleName"))
f.libId = Some(libId.getOrElse("noLibName"))
f.outputDir = new File(outputDir, "flexiprep")
(f.fastqR1Qc, f.fastqR2Qc)
}.getOrElse((read1, read2))
lazy protected val flexiprep: Option[Flexiprep] = if (!skipFlexiprep) {
Some(new Flexiprep(this))
} else None
/** Method to add jobs */
def biopetScript(): Unit = {
val (r1, r2): (File, Option[File]) = (fastqR1, fastqR2, bamFile) match {
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