Commit 4b16b7cd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Move defaults

parent fed34592
......@@ -28,6 +28,7 @@ import nl.lumc.sasc.biopet.scripts.SquishBed
import nl.lumc.sasc.biopet.tools.SageCountFastq
import nl.lumc.sasc.biopet.tools.SageCreateLibrary
import nl.lumc.sasc.biopet.tools.SageCreateTagCounts
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
......@@ -42,14 +43,21 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
var tagsLibrary: File = config("tags_library")
defaults ++= Map("bowtie" -> Map(
override def defaults = ConfigUtils.mergeMaps(Map("bowtie" -> Map(
"m" -> 1,
"k" -> 1,
"best" -> true,
"strata" -> true,
"seedmms" -> 1
), "mapping" -> Map(
"aligner" -> "bowtie",
"skip_flexiprep" -> true,
"skip_markduplicates" -> true
), "flexiprep" -> Map(
"skip_clip" -> true,
"skip_trim" -> true
)
)
), super.defaults)
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
......@@ -59,20 +67,12 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
val prefixFastq: File = new File(getLibraryDir, sampleId + "-" + libraryId + ".prefix.fastq")
val flexiprep = new Flexiprep(qscript)
flexiprep.skipClip = true
flexiprep.skipTrim = true
flexiprep.sampleName = sampleId
flexiprep.libraryName = libraryId
val mapping = new Mapping(qscript)
mapping.aligner = config("aligner", default = "bowtie")
mapping.skipFlexiprep = true
mapping.skipMarkduplicates = true
mapping.RGLB = libraryId
mapping.RGSM = sampleId
mapping.RGPL = config("PL")
mapping.RGPU = config("PU")
mapping.RGCN = config("CN")
mapping.libraryId = libraryId
mapping.sampleId = sampleId
def runJobs(): Unit = {
flexiprep.outputDir = getLibraryDir + "flexiprep/"
......
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