Commit f99780c7 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Refactor config values

parent cda35fd5
......@@ -36,23 +36,15 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
@Output(doc = "Output vcf", shortName = "o", required = false)
var outputVcf: File = _
var minSampleDepth: Option[Int] = _
var minTotalDepth: Option[Int] = _
var minAlternateDepth: Option[Int] = _
var minSamplesPass: Option[Int] = _
var filterRefCalls: Boolean = _
var minSampleDepth: Option[Int] = config("min_sample_depth")
var minTotalDepth: Option[Int] = config("min_total_depth")
var minAlternateDepth: Option[Int] = config("min_alternate_depth")
var minSamplesPass: Option[Int] = config("min_samples_pass")
var filterRefCalls: Boolean = config("filter_ref_calls")
override val defaultVmem = "8G"
memoryLimit = Option(4.0)
override def afterGraph {
minSampleDepth = config("min_sample_depth")
minTotalDepth = config("min_total_depth")
minAlternateDepth = config("min_alternate_depth")
minSamplesPass = config("min_samples_pass")
filterRefCalls = config("filter_ref_calls")
}
override def commandLine = super.commandLine +
required("-I", inputVcf) +
required("-o", outputVcf) +
......
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