Commit 625488b9 authored by Peter van 't Hof's avatar Peter van 't Hof

Remove duplicate tool list

parent 635a1a75
......@@ -111,6 +111,11 @@
<artifactId>Basty</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsPackage</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
......
......@@ -40,30 +40,5 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.basty.Basty
) ::: publicPipelines
def tools: List[MainCommand] = List(
nl.lumc.sasc.biopet.tools.MergeTables,
nl.lumc.sasc.biopet.tools.WipeReads,
nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
nl.lumc.sasc.biopet.tools.FastqSync,
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.VcfStats,
nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
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.tools.SeqStat,
nl.lumc.sasc.biopet.tools.VepNormalizer,
nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
nl.lumc.sasc.biopet.tools.VcfWithVcf,
nl.lumc.sasc.biopet.tools.ValidateFastq,
nl.lumc.sasc.biopet.tools.KrakenReportToJson)
def tools: List[MainCommand] = BiopetToolsExecutable.tools
}
......@@ -44,5 +44,7 @@ object BiopetToolsExecutable extends BiopetExecutable {
nl.lumc.sasc.biopet.tools.SeqStat,
nl.lumc.sasc.biopet.tools.VepNormalizer,
nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
nl.lumc.sasc.biopet.tools.VcfWithVcf)
nl.lumc.sasc.biopet.tools.VcfWithVcf,
nl.lumc.sasc.biopet.tools.ValidateFastq,
nl.lumc.sasc.biopet.tools.KrakenReportToJson)
}
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