BiopetExecutableMain.scala 2.66 KB
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/**
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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
  *
  * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
  * license; For commercial users or users who do not want to follow the AGPL
  * license, please contact us to obtain a separate license.
  */
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package nl.lumc.sasc.biopet

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import nl.lumc.sasc.biopet.core.jobreport.MergeQueueJobReports
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import nl.lumc.sasc.biopet.core.pipelinestatus.PipelineStatus
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import nl.lumc.sasc.biopet.utils.{BiopetExecutable, MainCommand}
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object BiopetExecutableMain extends BiopetExecutable {
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  def pipelines: List[MainCommand] = List(
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    nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
    nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
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    nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMapping,
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    nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
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    nl.lumc.sasc.biopet.pipelines.tinycap.TinyCap,
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    nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
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    nl.lumc.sasc.biopet.pipelines.sage.Sage,
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    nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig,
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    nl.lumc.sasc.biopet.pipelines.kopisu.Kopisu,
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    nl.lumc.sasc.biopet.pipelines.carp.Carp,
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    nl.lumc.sasc.biopet.pipelines.carp.PeakCalling,
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    nl.lumc.sasc.biopet.pipelines.toucan.Toucan,
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    nl.lumc.sasc.biopet.pipelines.shiva.ShivaSvCalling,
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    nl.lumc.sasc.biopet.pipelines.gears.GearsSingle,
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    nl.lumc.sasc.biopet.pipelines.gears.Gears,
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    nl.lumc.sasc.biopet.pipelines.gwastest.GwasTest,
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    nl.lumc.sasc.biopet.pipelines.gwastest.impute.Impute2Vcf,
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    nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
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    nl.lumc.sasc.biopet.pipelines.basty.Basty,
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    nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
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    nl.lumc.sasc.biopet.pipelines.tarmac.Tarmac,
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    nl.lumc.sasc.biopet.pipelines.shiva.GenotypeGvcfs,
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    nl.lumc.sasc.biopet.pipelines.generateindexes.DownloadGenomes,
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    nl.lumc.sasc.biopet.pipelines.generateindexes.GenerateIndexes,
    nl.lumc.sasc.biopet.pipelines.generateindexes.ValidateAnnotations
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  )
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  def tools: List[MainCommand] =
    MergeQueueJobReports :: PipelineStatus :: BiopetToolsExecutable.tools
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  def templates: List[MainCommand] = List(
    nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping,
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    nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva,
    nl.lumc.sasc.biopet.pipelines.gentrap.template.Gentrap
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  )
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}