Commit 7c40ad23 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Disable default library calling

parent 6e5dd48d
......@@ -116,10 +116,9 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
flexiprep.inputR2 = config("R2")
flexiprep.outputDir = new File(libDir, "flexiprep")
lazy val gs = new GearsSingle(qscript)
gs.sampleId = Some(sampleId)
gs.libId = Some(libId)
gs.outputDir = libDir
val libraryGears: Boolean = config("library_gears", default = false)
lazy val gearsSingle = if (libraryGears) Some(new GearsSingle(qscript)) else None
/** Function that add library jobs */
protected def addJobs(): Unit = {
......@@ -127,9 +126,15 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
flexiprep.inputR2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
add(flexiprep)
gs.fastqR1 = Some(addDownsample(flexiprep.fastqR1Qc, gs.outputDir))
gs.fastqR2 = flexiprep.fastqR2Qc.map(addDownsample(_, gs.outputDir))
add(gs)
gearsSingle.foreach { gs =>
gs.sampleId = Some(sampleId)
gs.libId = Some(libId)
gs.outputDir = libDir
gs.fastqR1 = Some(addDownsample(flexiprep.fastqR1Qc, gs.outputDir))
gs.fastqR2 = flexiprep.fastqR2Qc.map(addDownsample(_, gs.outputDir))
add(gs)
}
}
/** Must return files to store into summary */
......
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