BiopetToolsExecutable.scala 2.33 KB
Newer Older
Peter van 't Hof's avatar
Peter van 't Hof committed
1
2
3
4
5
6
7
8
9
10
/**
 * 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
 *
11
 * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
Peter van 't Hof's avatar
Peter van 't Hof committed
12
13
14
15
16
17
18
19
20
21
22
23
 * 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

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

object BiopetToolsExecutable extends BiopetExecutable {

  def pipelines: List[MainCommand] = Nil

  def tools: List[MainCommand] = List(
24
    nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
25
    nl.lumc.sasc.biopet.tools.bamstats.BamStats,
26
27
28
    nl.lumc.sasc.biopet.tools.BaseCounter,
    nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
    nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
29
    nl.lumc.sasc.biopet.tools.flagstat.BiopetFlagstat,
Peter van 't Hof's avatar
Peter van 't Hof committed
30
    nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
31
32
33
    nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
    nl.lumc.sasc.biopet.tools.FastqSplitter,
    nl.lumc.sasc.biopet.tools.FastqSync,
Peter van 't Hof's avatar
Peter van 't Hof committed
34
    nl.lumc.sasc.biopet.tools.FastqFilter,
Peter van 't Hof's avatar
Peter van 't Hof committed
35
    nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
Peter van 't Hof's avatar
Peter van 't Hof committed
36
    nl.lumc.sasc.biopet.tools.FindOverlapMatch,
37
38
39
    nl.lumc.sasc.biopet.tools.GvcfToBed,
    nl.lumc.sasc.biopet.tools.MergeAlleles,
    nl.lumc.sasc.biopet.tools.MergeTables,
Peter van 't Hof's avatar
Peter van 't Hof committed
40
    nl.lumc.sasc.biopet.tools.MpileupToVcf,
41
    nl.lumc.sasc.biopet.tools.PrefixFastq,
Peter van 't Hof's avatar
Peter van 't Hof committed
42
    nl.lumc.sasc.biopet.tools.SageCountFastq,
43
    nl.lumc.sasc.biopet.tools.SamplesTsvToConfig,
Peter van 't Hof's avatar
Peter van 't Hof committed
44
    nl.lumc.sasc.biopet.tools.SeqStat,
45
46
    nl.lumc.sasc.biopet.tools.SquishBed,
    nl.lumc.sasc.biopet.tools.SummaryToTsv,
Peter van 't Hof's avatar
Peter van 't Hof committed
47
    nl.lumc.sasc.biopet.tools.ValidateFastq,
48
    nl.lumc.sasc.biopet.tools.ValidateVcf,
49
50
51
52
53
    nl.lumc.sasc.biopet.tools.VcfFilter,
    nl.lumc.sasc.biopet.tools.VcfStats,
    nl.lumc.sasc.biopet.tools.VcfToTsv,
    nl.lumc.sasc.biopet.tools.VcfWithVcf,
    nl.lumc.sasc.biopet.tools.VepNormalizer,
Peter van 't Hof's avatar
Peter van 't Hof committed
54
55
    nl.lumc.sasc.biopet.tools.WipeReads,
    nl.lumc.sasc.biopet.tools.DownloadNcbiAssembly)
Peter van 't Hof's avatar
Peter van 't Hof committed
56
}