Commit fa32164f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change some options

parent fd8a4043
......@@ -36,11 +36,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
var countBed: Option[File] = config("count_bed")
var squishedCountBed: Option[File] = config("squished_count_bed")
var squishedCountBed: File = _
var transcriptome: Option[File] = config("transcriptome")
var tagsLibrary: Option[File] = config("tags_library")
override def defaults = ConfigUtils.mergeMaps(Map("bowtie" -> Map(
......@@ -129,16 +126,14 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
if (!outputDir.endsWith("/")) outputDir += "/"
if (transcriptome.isEmpty && tagsLibrary.isEmpty)
throw new IllegalStateException("No transcriptome or taglib found")
if (countBed.isEmpty && squishedCountBed.isEmpty)
throw new IllegalStateException("No bedfile supplied, please add a countBed or squishedCountBed")
if (countBed.isEmpty)
throw new IllegalStateException("No bedfile supplied, please add a countBed")
}
def biopetScript() {
if (squishedCountBed.isEmpty) {
val squishBed = SquishBed(this, countBed.get, outputDir)
add(squishBed)
squishedCountBed = Some(squishBed.output)
}
val squishBed = SquishBed(this, countBed.get, outputDir)
add(squishBed)
squishedCountBed = squishBed.output
if (tagsLibrary.isEmpty) {
val cdl = new SageCreateLibrary(this)
......@@ -158,19 +153,19 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
def addBedtoolsCounts(bamFile: File, outputPrefix: String, outputDir: String) {
val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed.get, outputDir + outputPrefix + ".genome.sense.coverage",
val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed, outputDir + outputPrefix + ".genome.sense.coverage",
depth = false, sameStrand = true, diffStrand = false)
val countSense = new BedtoolsCoverageToCounts(this)
countSense.input = bedtoolsSense.output
countSense.output = outputDir + outputPrefix + ".genome.sense.counts"
val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed.get, outputDir + outputPrefix + ".genome.antisense.coverage",
val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed, outputDir + outputPrefix + ".genome.antisense.coverage",
depth = false, sameStrand = false, diffStrand = true)
val countAntisense = new BedtoolsCoverageToCounts(this)
countAntisense.input = bedtoolsAntisense.output
countAntisense.output = outputDir + outputPrefix + ".genome.antisense.counts"
val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed.get, outputDir + outputPrefix + ".genome.coverage",
val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed, outputDir + outputPrefix + ".genome.coverage",
depth = false, sameStrand = false, diffStrand = false)
val count = new BedtoolsCoverageToCounts(this)
count.input = bedtools.output
......
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