Commit 6d77359f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added default values for bowtie

parent 998da3a9
......@@ -26,6 +26,15 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
var tagsLibrary : File = _
defaults ++= Map("bowtie" -> Map(
"m" -> 1,
"k" -> 1,
"best" -> true,
"strata" -> true,
"seedmms" -> 1
)
)
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
if (!outputDir.endsWith("/")) outputDir += "/"
......@@ -41,7 +50,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def biopetScript() {
if (squishedCountBed == null) {
val squishBed = SquishBed.apply(this, countBed, outputDir)
val squishBed = SquishBed(this, countBed, outputDir)
add(squishBed)
squishedCountBed = squishBed.output
}
......
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