Pindel.scala 2.25 KB
Newer Older
Wai Yi Leung's avatar
Wai Yi Leung committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
/**
 * 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.
 */
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers

Wai Yi Leung's avatar
Wai Yi Leung committed
18
19
import java.text.SimpleDateFormat
import java.util.Calendar
Wai Yi Leung's avatar
Wai Yi Leung committed
20

Wai Yi Leung's avatar
Wai Yi Leung committed
21
import nl.lumc.sasc.biopet.extensions.pindel._
Wai Yi Leung's avatar
Wai Yi Leung committed
22
23
24
25
26
27
import nl.lumc.sasc.biopet.utils.config.Configurable

/// Pindel is actually a mini pipeline executing binaries from the pindel package
class Pindel(val root: Configurable) extends SvCaller {
  val name = "pindel"

28
  /** Default pipeline config */
29
30
  override def defaults = Map(
    "pindelvcf" -> Map(
31
32
      "rdate" -> new SimpleDateFormat("yyyyMMdd").format(Calendar.getInstance().getTime()),
      "compact_output_limit" -> 10
33
    ))
34

Wai Yi Leung's avatar
Wai Yi Leung committed
35
36
37
38
  def biopetScript() {
    for ((sample, bamFile) <- inputBams) {
      val pindelDir = new File(outputDir, sample)

Wai Yi Leung's avatar
Wai Yi Leung committed
39
      val config_file: File = new File(pindelDir, sample + ".pindel.cfg")
Wai Yi Leung's avatar
Wai Yi Leung committed
40
41
42
43
44
45
46
47
      val cfg = new PindelConfig(this)
      cfg.input = bamFile
      cfg.sampleName = sample
      cfg.output = config_file
      add(cfg)

      val pindel = PindelCaller(this, cfg.output, pindelDir)
      add(pindel)
Wai Yi Leung's avatar
Wai Yi Leung committed
48
49
50
51
52
53

      // Current date
      val today = Calendar.getInstance().getTime()
      val todayformat = new SimpleDateFormat("yyyyMMdd")

      val pindelVcf = new PindelVCF(this)
Wai Yi Leung's avatar
Wai Yi Leung committed
54
      pindelVcf.deps ::= pindel.outputFile
55
56
57
      pindelVcf.pindelOutputInputHolder = pindel.outputFile
      pindelVcf.pindelOutputRoot = Some(new File(pindelDir, "sample"))
      pindelVcf.rDate = todayformat.format(today) // officially, we should enter the date of the genome here
Wai Yi Leung's avatar
Wai Yi Leung committed
58
59
      pindelVcf.outputVCF = new File(pindelDir, s"${sample}.pindel.vcf")
      add(pindelVcf)
Wai Yi Leung's avatar
Wai Yi Leung committed
60
61
62
63
    }

  }
}