Commit 5de27e08 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge branch 'develop' into fix-BIOPET-649

parents 988d35a6 8fa9668a
......@@ -206,7 +206,9 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
val foundAdapters = modules.get("Adapter Content").map { x =>
val header = x.lines.head.split("\t").tail.zipWithIndex
val lines = x.lines.tail.map(_.split("\t").tail)
val found = header.filter(h => lines.exists(x => x(h._2).toFloat > 0)).map(_._1)
val found = header
.filter(h => lines.exists(x => x(h._2).toFloat > adapterCutoff))
.map(_._1)
adapterSet.filter(x => found.contains(x.name))
}
......@@ -214,6 +216,8 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
} else Set()
}
val adapterCutoff: Float = config("adapter_cutoff", default = 0.001)
@Output
private var outputFiles: List[File] = Nil
......
......@@ -36,11 +36,6 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller {
override def fixedValues = Map("haplotypecaller" -> Map("emitRefConfidence" -> "GVCF"))
override def defaults = Map("haplotypecaller" -> Map(
"variant_index_type" -> "LINEAR",
"variant_index_parameter" -> 128000)
)
def biopetScript() {
gVcfFiles = for ((sample, inputBam) <- inputBams) yield {
val hc = gatk.HaplotypeCaller(this, List(inputBam), new File(outputDir, sample + ".gvcf.vcf.gz"))
......
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