BiopetToolsExecutable.scala 2.34 KB
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/**
 * Biopet is built on top of GATK Queue for building bioinformatic
 * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
 * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
 * should also be able to execute Biopet tools and pipelines.
 *
 * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
 *
 * Contact us at: sasc@lumc.nl
 *
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 * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
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 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
package nl.lumc.sasc.biopet

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import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
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object BiopetToolsExecutable extends BiopetExecutable {

  def pipelines: List[MainCommand] = Nil

  def tools: List[MainCommand] = List(
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    nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
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    nl.lumc.sasc.biopet.tools.bamstats.BamStats,
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    nl.lumc.sasc.biopet.tools.BaseCounter,
    nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
    nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
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    nl.lumc.sasc.biopet.tools.flagstat.BiopetFlagstat,
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    nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
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    nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
    nl.lumc.sasc.biopet.tools.FastqSplitter,
    nl.lumc.sasc.biopet.tools.FastqSync,
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    nl.lumc.sasc.biopet.tools.FastqFilter,
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    nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
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    nl.lumc.sasc.biopet.tools.FindOverlapMatch,
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    nl.lumc.sasc.biopet.tools.GvcfToBed,
    nl.lumc.sasc.biopet.tools.MergeAlleles,
    nl.lumc.sasc.biopet.tools.MergeTables,
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    nl.lumc.sasc.biopet.tools.MpileupToVcf,
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    nl.lumc.sasc.biopet.tools.PrefixFastq,
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    nl.lumc.sasc.biopet.tools.SageCountFastq,
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    nl.lumc.sasc.biopet.tools.SamplesTsvToConfig,
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    nl.lumc.sasc.biopet.tools.SeqStat,
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    nl.lumc.sasc.biopet.tools.SquishBed,
    nl.lumc.sasc.biopet.tools.SummaryToTsv,
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    nl.lumc.sasc.biopet.tools.ValidateFastq,
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    nl.lumc.sasc.biopet.tools.ValidateVcf,
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    nl.lumc.sasc.biopet.tools.VcfFilter,
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    nl.lumc.sasc.biopet.tools.vcfstats.VcfStats,
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    nl.lumc.sasc.biopet.tools.VcfToTsv,
    nl.lumc.sasc.biopet.tools.VcfWithVcf,
    nl.lumc.sasc.biopet.tools.VepNormalizer,
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    nl.lumc.sasc.biopet.tools.WipeReads,
    nl.lumc.sasc.biopet.tools.DownloadNcbiAssembly)
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}