Commit e93bf522 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added samtoolsview options to fixedvalues

parent fe662220
......@@ -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.{BuildBamIndex, 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
......@@ -46,7 +46,14 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
),
"samtoolsview" -> Map("q" -> 10)
)
override def fixedValues = Map(
"samtoolsview" -> Map(
"h" -> true,
"b" -> true
)
)
def summaryFile = new File(outputDir, "Carp.summary.json")
//TODO: Add summary
......@@ -122,8 +129,6 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
val samtoolsView = new SamtoolsView(qscript)
samtoolsView.input = bamFile
samtoolsView.output = bamFileFilter
samtoolsView.b = true
samtoolsView.h = true
add(samtoolsView)
val buildBamIndex = new BuildBamIndex(qscript)
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment