Commit 292cae4e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Switch to squishBed tool

parent 63090796
......@@ -2,10 +2,10 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import nl.lumc.sasc.biopet.core.{ToolCommandFuntion, ToolCommand}
import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import org.broadinstitute.gatk.utils.commandline.{Output, Input}
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvanthof on 22/08/15.
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.scripts.SquishBed
import nl.lumc.sasc.biopet.tools.SquishBed
import nl.lumc.sasc.biopet.tools.{ BedtoolsCoverageToCounts, PrefixFastq, SageCountFastq, SageCreateLibrary, SageCreateTagCounts }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
......@@ -49,7 +49,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
), "flexiprep" -> Map(
"skip_clip" -> true,
"skip_trim" -> true
)
), "strandSensitive" -> true
), super.defaults)
def summaryFile: File = new File(outputDir, "Sage.summary.json")
......@@ -146,7 +146,9 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
def biopetScript() {
val squishBed = SquishBed(this, countBed.get, outputDir)
val squishBed = new SquishBed(this)
squishBed.input = countBed.get
squishBed.output = new File(outputDir, countBed.get.getName.stripSuffix(".bed") + ".squish.bed")
add(squishBed)
squishedCountBed = squishBed.output
......
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