Commit 9d05586a authored by rhpvorderman's avatar rhpvorderman

Merge remote-tracking branch 'origin' into Fix-BIOPET-572

parents ae0a5dfd 1f2295c2
......@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
var reference: File = null
var reference: File = _
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
......@@ -42,7 +42,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var k: Option[Int] = config("k")
var r: Option[Float] = config("r")
var S: Boolean = config("S", default = false)
var M: Boolean = config("M", default = true)
var M: Boolean = config("M", default = false)
var w: Option[Int] = config("w")
var d: Option[Int] = config("d")
var c: Option[Int] = config("c")
......@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
if (reference == null) reference = referenceFasta()
}
def cmdLine = {
def cmdLine: String = {
required(executable) +
required("mem") +
optional("-k", k) +
......
......@@ -38,6 +38,8 @@ class CleverFixVCF(val parent: Configurable) extends BiopetJavaCommandLineFuncti
@Argument(doc = "Samplename")
var sampleName: String = _
override def defaultCoreMemory = 4.0
override def cmdLine = super.cmdLine +
required("-i", input) +
required("-o", output) +
......
......@@ -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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