BiopetExecutablePublic.scala 2.64 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
 *
 * A dual licensing mode is applied. The source code within this project that are
 * not part of GATK Queue 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.core

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object BiopetExecutablePublic extends BiopetExecutable {
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  def protectedPipelines: 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.gentrap.Gentrap,
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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.carp.Carp,
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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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  )
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  def pipelines: List[MainCommand] = List(
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    nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
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    nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
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    nl.lumc.sasc.biopet.pipelines.basty.Basty,
    nl.lumc.sasc.biopet.pipelines.gears.Gears
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  ) ::: protectedPipelines
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  def tools: List[MainCommand] = List(
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    nl.lumc.sasc.biopet.tools.MergeTables,
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    nl.lumc.sasc.biopet.tools.WipeReads,
    nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
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    nl.lumc.sasc.biopet.tools.FastqSync,
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    nl.lumc.sasc.biopet.tools.BiopetFlagstat,
    nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
    nl.lumc.sasc.biopet.tools.VcfToTsv,
    nl.lumc.sasc.biopet.tools.VcfFilter,
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    nl.lumc.sasc.biopet.tools.VcfStats,
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    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,
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    nl.lumc.sasc.biopet.tools.MergeAlleles,
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    nl.lumc.sasc.biopet.tools.SamplesTsvToJson,
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    nl.lumc.sasc.biopet.tools.SeqStat,
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    nl.lumc.sasc.biopet.tools.VepNormalizer,
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    nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
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    nl.lumc.sasc.biopet.tools.VcfWithVcf)
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}