Commit 73995acb authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Updated Executable

parent 51f729f1
...@@ -7,12 +7,12 @@ package nl.lumc.sasc.biopet.core ...@@ -7,12 +7,12 @@ package nl.lumc.sasc.biopet.core
object BiopetExecutableProtected extends BiopetExecutable { object BiopetExecutableProtected extends BiopetExecutable {
def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List( def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List(
nl.lumc.sasc.biopet.pipelines.gatk.GatkBenchmarkGenotyping,
nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping, nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling, nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline, nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration, nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
nl.lumc.sasc.biopet.pipelines.gatk.ShivaGatk, nl.lumc.sasc.biopet.pipelines.gatk.ShivaGatk,
nl.lumc.sasc.biopet.pipelines.gatk.ShivaVariantcallingGatk,
nl.lumc.sasc.biopet.pipelines.basty.Basty) nl.lumc.sasc.biopet.pipelines.basty.Basty)
def tools = BiopetExecutablePublic.tools def tools = BiopetExecutablePublic.tools
......
...@@ -27,7 +27,8 @@ object BiopetExecutablePublic extends BiopetExecutable { ...@@ -27,7 +27,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.kopisu.ConiferPipeline, nl.lumc.sasc.biopet.pipelines.kopisu.ConiferPipeline,
nl.lumc.sasc.biopet.pipelines.carp.Carp, nl.lumc.sasc.biopet.pipelines.carp.Carp,
nl.lumc.sasc.biopet.pipelines.toucan.Toucan, nl.lumc.sasc.biopet.pipelines.toucan.Toucan,
nl.lumc.sasc.biopet.pipelines.shiva.Shiva nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
) )
def tools: List[MainCommand] = List( def tools: List[MainCommand] = List(
......
...@@ -193,7 +193,6 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript { ...@@ -193,7 +193,6 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
addAll(bamMetrics.functions) addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics) addSummaryQScript(bamMetrics)
if (config("single_sample_variantcalling", default = false).asBoolean) { if (config("single_sample_variantcalling", default = false).asBoolean) {
val vc = makeVariantcalling(multisample = false) val vc = makeVariantcalling(multisample = false)
vc.sampleId = Some(sampleId) vc.sampleId = Some(sampleId)
......
...@@ -5,7 +5,7 @@ import java.io.File ...@@ -5,7 +5,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag } import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.summary.SummaryQScript import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.tools.{VcfStats, VcfFilter, MpileupToVcf} import nl.lumc.sasc.biopet.tools.{ VcfStats, VcfFilter, MpileupToVcf }
import nl.lumc.sasc.biopet.utils.ConfigUtils import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.Input import org.broadinstitute.gatk.utils.commandline.Input
......
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