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