Commit 81fd15f8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added defaultAligner var

parent 7b626832
......@@ -77,16 +77,12 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var RGPI: Int = _
var paired: Boolean = false
var defaultAligner = "bwa"
val flexiprep = new Flexiprep(this)
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
var inputtype: String = config("inputtype", "dna")
if (aligner == null) {
if (inputtype == "rna") aligner = config("aligner", "star-2pass")
else aligner = config("aligner", "bwa")
}
if (aligner == null) aligner = config("aligner", default = defaultAligner)
if (reference == null) reference = config("reference")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on mapping module")
else if (!outputDir.endsWith("/")) outputDir += "/"
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment