Commit e671341e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Protected copy content from public

parent 5a474415
......@@ -25,6 +25,11 @@
<artifactId>BiopetFramework</artifactId>
<version>0.2.0-DEV</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetPublicPackage</artifactId>
<version>0.2.0-DEV</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatkPipelines</artifactId>
......
package nl.lumc.sasc.biopet.core
object BiopetExecutableProtected extends BiopetExecutable {
lazy val pipelines: List[MainCommand] = List(
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
trait BiopetExecutableProtected extends BiopetExecutablePublic {
override def pipelines: List[MainCommand] = super.pipelines ::: List(
nl.lumc.sasc.biopet.pipelines.gatk.GatkBenchmarkGenotyping,
nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVcfSampleCompare,
nl.lumc.sasc.biopet.pipelines.sage.Sage,
nl.lumc.sasc.biopet.pipelines.basty.Basty,
nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp)
lazy val tools: List[MainCommand] = List(
nl.lumc.sasc.biopet.tools.WipeReads,
nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
nl.lumc.sasc.biopet.tools.BiopetFlagstat,
nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
nl.lumc.sasc.biopet.tools.VcfToTsv,
nl.lumc.sasc.biopet.tools.VcfFilter,
nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
nl.lumc.sasc.biopet.tools.BedToInterval,
nl.lumc.sasc.biopet.tools.MpileupToVcf,
nl.lumc.sasc.biopet.tools.FastqSplitter,
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
nl.lumc.sasc.biopet.tools.SageCountFastq,
nl.lumc.sasc.biopet.tools.SageCreateLibrary,
nl.lumc.sasc.biopet.tools.SageCreateTagCounts,
nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
nl.lumc.sasc.biopet.tools.MergeAlleles,
nl.lumc.sasc.biopet.tools.SamplesTsvToJson)
nl.lumc.sasc.biopet.pipelines.basty.Basty)
}
......@@ -5,9 +5,9 @@ import org.apache.log4j.Logger
trait BiopetExecutable extends Logging {
val pipelines: List[MainCommand]
def pipelines: List[MainCommand]
val tools: List[MainCommand]
def tools: List[MainCommand]
val modules: Map[String, List[MainCommand]] = Map(
"pipeline" -> pipelines,
......
package nl.lumc.sasc.biopet.core
object BiopetExecutablePublic extends BiopetExecutable {
lazy val pipelines: List[MainCommand] = List(
trait BiopetExecutablePublic extends BiopetExecutable {
def pipelines: List[MainCommand] = List(
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
......@@ -9,7 +9,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.sage.Sage,
nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp)
lazy val tools: List[MainCommand] = List(
def tools: List[MainCommand] = List(
nl.lumc.sasc.biopet.tools.WipeReads,
nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
nl.lumc.sasc.biopet.tools.BiopetFlagstat,
......
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