Commit c73d6b1d authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

import deps

parent 1df0636d
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.config._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import nl.lumc.sasc.biopet.extensions.picard.{BuildBamIndex, MergeSamFiles}
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
......@@ -128,6 +128,11 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
samtoolsView.h = true
add(samtoolsView)
val buildBamIndex = new BuildBamIndex(qscript)
buildBamIndex.input = bamFileFilter
buildBamIndex.output = swapExt(bamFileFilter.getParent, bamFileFilter, ".bam", ".bai")
add(buildBamIndex)
val macs2 = new Macs2CallPeak(qscript)
macs2.treatment = bamFileFilter
macs2.name = Some(sampleId)
......
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