BiopetExecutableMain.scala 1.99 KB
Newer Older
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
12
13
14
 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
15
16
package nl.lumc.sasc.biopet

Peter van 't Hof's avatar
Peter van 't Hof committed
17
import nl.lumc.sasc.biopet.pipelines.generateindexes.DownloadGenomes$
Peter van 't Hof's avatar
Peter van 't Hof committed
18
import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
19

Peter van 't Hof's avatar
Peter van 't Hof committed
20
object BiopetExecutableMain extends BiopetExecutable {
Peter van 't Hof's avatar
Peter van 't Hof committed
21
  def pipelines: List[MainCommand] = List(
22
23
    nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
    nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
24
    nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMapping,
Peter van 't Hof's avatar
Peter van 't Hof committed
25
    nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
Peter van 't Hof's avatar
Peter van 't Hof committed
26
    nl.lumc.sasc.biopet.pipelines.tinycap.TinyCap,
27
    nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
28
    nl.lumc.sasc.biopet.pipelines.sage.Sage,
29
    nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig,
30
    nl.lumc.sasc.biopet.pipelines.kopisu.Kopisu,
Sander Bollen's avatar
Sander Bollen committed
31
    nl.lumc.sasc.biopet.pipelines.carp.Carp,
Peter van 't Hof's avatar
Peter van 't Hof committed
32
    nl.lumc.sasc.biopet.pipelines.toucan.Toucan,
33
    nl.lumc.sasc.biopet.pipelines.shiva.ShivaSvCalling,
Peter van 't Hof's avatar
Peter van 't Hof committed
34
    nl.lumc.sasc.biopet.pipelines.gears.GearsSingle,
35
    nl.lumc.sasc.biopet.pipelines.gears.Gears,
36
    nl.lumc.sasc.biopet.pipelines.gwastest.GwasTest,
37
    nl.lumc.sasc.biopet.pipelines.gwastest.impute.Impute2Vcf,
38
    nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
Peter van 't Hof's avatar
Peter van 't Hof committed
39
    nl.lumc.sasc.biopet.pipelines.basty.Basty,
40
    nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
Peter van 't Hof's avatar
Peter van 't Hof committed
41
    DownloadGenomes
Peter van 't Hof's avatar
Peter van 't Hof committed
42
  )
43

Peter van 't Hof's avatar
Peter van 't Hof committed
44
  def tools: List[MainCommand] = BiopetToolsExecutable.tools
45
}