Commit 6ac5e2c8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

format

parent 3b0bbaf7
......@@ -24,11 +24,10 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
defaults ++= Map("ploidy" -> 1, "use_haplotypecaller" -> false, "use_unifiedgenotyper" -> true, "joint_variantcalling" -> true)
var gatkPipeline: GatkPipeline = _
var gatkPipeline: GatkPipeline = new GatkPipeline(this)
gatkPipeline.jointVariantcalling = true
def init() {
gatkPipeline = new GatkPipeline(this)
gatkPipeline.outputDir = outputDir
gatkPipeline.init
}
......@@ -51,7 +50,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
add(catConsensus)
val catConsensusSnps = Cat(this, refVariantSnps.consensus :: samplesOutput.map(_._2.outputSnps.consensus).toList, outputDir + "fastas/consensus.snps_only.fasta")
add(catConsensusSnps)
val catConsensusVariants = Cat(this, refVariants.consensusVariants :: samplesOutput.map(_._2.output.consensusVariants).toList, outputDir + "fastas/consensus.variant.fasta")
add(catConsensusVariants)
val catConsensusVariantsSnps = Cat(this, refVariantSnps.consensusVariants :: samplesOutput.map(_._2.outputSnps.consensusVariants).toList, outputDir + "fastas/consensus.variant.snps_only.fasta")
......
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