Commit 23a9cd94 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'develop' into feature-scoverage

parents b62255f7 aca99bf8
......@@ -153,11 +153,11 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
scriptOutput.rawVcfFile = m2v.output
val vcfFilter = new VcfFilter(this) {
override def defaults = ConfigUtils.mergeMaps(Map("min_sample_depth" -> 8,
override def defaults = Map("min_sample_depth" -> 8,
"min_alternate_depth" -> 2,
"min_samples_pass" -> 1,
"filter_ref_calls" -> true
), super.defaults)
)
}
vcfFilter.inputVcf = m2v.output
vcfFilter.outputVcf = swapExt(outputDir, m2v.output, ".vcf", ".filter.vcf.gz")
......
......@@ -35,10 +35,10 @@ trait BastyTrait extends MultiSampleQScript {
def variantcallers = List("freebayes")
override def defaults = ConfigUtils.mergeMaps(Map(
override def defaults = Map(
"ploidy" -> 1,
"variantcallers" -> variantcallers
), super.defaults)
)
lazy val shiva: ShivaTrait = new Shiva(qscript)
......
......@@ -47,7 +47,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
override def defaultCoreMemory = 4.0
override def defaultThreads = 8
var sam: Boolean = config("sam", default = true)
var sam: Boolean = config("sam", default = false)
var sam_RG: Option[String] = config("sam-RG")
var seedlen: Option[Int] = config("seedlen")
var seedmms: Option[Int] = config("seedmms")
......
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