BamMetrics.scala 8.55 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
17
package nl.lumc.sasc.biopet.pipelines.bammetrics

import java.io.File
Peter van 't Hof's avatar
Peter van 't Hof committed
18

Peter van 't Hof's avatar
Peter van 't Hof committed
19
import nl.lumc.sasc.biopet.core.annotations.{ AnnotationRefFlat, RibosomalRefFlat }
Peter van 't Hof's avatar
Peter van 't Hof committed
20
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
Peter van 't Hof's avatar
Peter van 't Hof committed
21
22
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect, BedtoolsSort }
Peter van 't Hof's avatar
Peter van 't Hof committed
23
import nl.lumc.sasc.biopet.extensions.picard._
24
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
Peter van 't Hof's avatar
Peter van 't Hof committed
25
import nl.lumc.sasc.biopet.extensions.tools.{ BamStats, BiopetFlagstat }
Sander Bollen's avatar
Sander Bollen committed
26
27
import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import nl.lumc.sasc.biopet.utils.config.Configurable
28
import nl.lumc.sasc.biopet.utils.intervals.BedCheck
Peter van 't Hof's avatar
Peter van 't Hof committed
29
import org.broadinstitute.gatk.queue.QScript
30

31
32
33
class BamMetrics(val root: Configurable) extends QScript
  with SummaryQScript
  with SampleLibraryTag
34
  with Reference
35
36
37
  with TargetRegions
  with AnnotationRefFlat
  with RibosomalRefFlat {
38

39
40
41
42
43
  def this() = this(null)

  @Input(doc = "Bam File", shortName = "BAM", required = true)
  var inputBam: File = _

44
45
  override def defaults = Map("bedtoolscoverage" -> Map("sorted" -> true))

Peter van 't Hof's avatar
Peter van 't Hof committed
46
  /** return location of summary file */
Peter van 't Hof's avatar
Peter van 't Hof committed
47
  def summaryFile = (sampleId, libId) match {
Peter van 't Hof's avatar
Peter van 't Hof committed
48
49
50
    case (Some(s), Some(l)) => new File(outputDir, s + "-" + l + ".BamMetrics.summary.json")
    case (Some(s), _)       => new File(outputDir, s + ".BamMetrics.summary.json")
    case _                  => new File(outputDir, "BamMetrics.summary.json")
Peter van 't Hof's avatar
Peter van 't Hof committed
51
52
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
53
  /** returns files to store in summary */
54
55
  def summaryFiles = Map("reference" -> referenceFasta(),
    "input_bam" -> inputBam) ++
Peter van 't Hof's avatar
Peter van 't Hof committed
56
57
    ampliconBedFile.map("amplicon" -> _).toMap ++
    ampliconBedFile.map(x => "roi_" + x.getName.stripSuffix(".bed") -> x).toMap
Peter van 't Hof's avatar
Peter van 't Hof committed
58

Peter van 't Hof's avatar
Peter van 't Hof committed
59
  /** return settings */
Peter van 't Hof's avatar
Peter van 't Hof committed
60
61
  def summarySettings = Map("amplicon_name" -> ampliconBedFile.collect { case x => x.getName.stripSuffix(".bed") },
    "roi_name" -> roiBedFiles.map(_.getName.stripSuffix(".bed")))
Peter van 't Hof's avatar
Peter van 't Hof committed
62

63
64
65
66
67
68
69
  override def reportClass = {
    val bammetricsReport = new BammetricsReport(this)
    bammetricsReport.outputDir = new File(outputDir, "report")
    bammetricsReport.summaryFile = summaryFile
    bammetricsReport.args = if (libId.isDefined) Map(
      "sampleId" -> sampleId.getOrElse("."),
      "libId" -> libId.getOrElse("."))
Peter van 't Hof's avatar
Peter van 't Hof committed
70
    else Map("sampleId" -> sampleId.getOrElse("."))
71
72
73
    Some(bammetricsReport)
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
74
  /** executed before script */
75
  def init(): Unit = {
Peter van 't Hof's avatar
Peter van 't Hof committed
76
    inputFiles :+= new InputFile(inputBam)
Peter van 't Hof's avatar
Peter van 't Hof committed
77
78
    ampliconBedFile.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
    roiBedFiles.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
79
80
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
81
  /** Script to add jobs */
82
  def biopetScript() {
83
    add(SamtoolsFlagstat(this, inputBam, outputDir))
84

85
86
87
88
    val bamStats = new BamStats(this)
    bamStats.bamFile = inputBam
    bamStats.outputDir = new File(outputDir, "bamstats")
    add(bamStats)
Peter van 't Hof's avatar
Peter van 't Hof committed
89
    addSummarizable(bamStats, "bamstats")
90

Peter van 't Hof's avatar
Peter van 't Hof committed
91
92
93
94
    val multiMetrics = new CollectMultipleMetrics(this)
    multiMetrics.input = inputBam
    multiMetrics.outputName = new File(outputDir, inputBam.getName.stripSuffix(".bam"))
    add(multiMetrics)
95
    addSummarizable(multiMetrics, "multi_metrics")
96

97
98
99
    val gcBiasMetrics = CollectGcBiasMetrics(this, inputBam, outputDir)
    add(gcBiasMetrics)
    addSummarizable(gcBiasMetrics, "gc_bias")
100

101
    if (config("wgs_metrics", default = true)) {
bow's avatar
bow committed
102
103
104
105
106
107
      val wgsMetrics = new CollectWgsMetrics(this)
      wgsMetrics.input = inputBam
      wgsMetrics.output = swapExt(outputDir, inputBam, ".bam", ".wgs.metrics")
      add(wgsMetrics)
      addSummarizable(wgsMetrics, "wgs")
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
108

109
    if (config("rna_metrics", default = false)) {
Peter van 't Hof's avatar
Peter van 't Hof committed
110
111
112
113
      val rnaMetrics = new CollectRnaSeqMetrics(this)
      rnaMetrics.input = inputBam
      rnaMetrics.output = swapExt(outputDir, inputBam, ".bam", ".rna.metrics")
      rnaMetrics.chartOutput = Some(swapExt(outputDir, inputBam, ".bam", ".rna.metrics.pdf"))
114
115
      rnaMetrics.refFlat = annotationRefFlat()
      rnaMetrics.ribosomalIntervals = ribosomalRefFlat()
Peter van 't Hof's avatar
Peter van 't Hof committed
116
      add(rnaMetrics)
117
      addSummarizable(rnaMetrics, "rna")
Peter van 't Hof's avatar
Peter van 't Hof committed
118
119
    }

Peter van 't Hof's avatar
Peter van 't Hof committed
120
121
122
123
124
125
126
127
128
129
130
131
132
    case class Intervals(bed: File, intervals: File)

    // Create temp jobs to convert bed files to intervals lists
    val roiIntervals = roiBedFiles.map(roiBedFile => {
      val roiIntervals = swapExt(outputDir, roiBedFile, ".bed", ".intervals")
      val ampBedToInterval = BedToIntervalList(this, roiBedFile, roiIntervals)
      ampBedToInterval.isIntermediate = true
      add(ampBedToInterval)
      Intervals(roiBedFile, roiIntervals)
    })

    // Metrics that require a amplicon bed file
    val ampIntervals = ampliconBedFile.collect {
Peter van 't Hof's avatar
Peter van 't Hof committed
133
134
135
      case bedFile =>
        val ampIntervals = swapExt(outputDir, bedFile, ".bed", ".intervals")
        val ampBedToInterval = BedToIntervalList(this, bedFile, ampIntervals)
Peter van 't Hof's avatar
Peter van 't Hof committed
136
137
138
        ampBedToInterval.isIntermediate = true
        add(ampBedToInterval)

139
        val chsMetrics = CollectHsMetrics(this, inputBam,
Peter van 't Hof's avatar
Peter van 't Hof committed
140
141
          List(ampIntervals), ampIntervals :: roiIntervals.map(_.intervals), outputDir)
        add(chsMetrics)
142
        addSummarizable(chsMetrics, "hs_metrics")
143

Peter van 't Hof's avatar
Peter van 't Hof committed
144
145
146
        val pcrMetrics = CollectTargetedPcrMetrics(this, inputBam,
          ampIntervals, ampIntervals :: roiIntervals.map(_.intervals), outputDir)
        add(pcrMetrics)
bow's avatar
bow committed
147
        addSummarizable(pcrMetrics, "targeted_pcr_metrics")
Peter van 't Hof's avatar
Peter van 't Hof committed
148

Peter van 't Hof's avatar
Peter van 't Hof committed
149
        Intervals(bedFile, ampIntervals)
Peter van 't Hof's avatar
Peter van 't Hof committed
150
151
152
153
    }

    // Create stats and coverage plot for each bed/interval file
    for (intervals <- roiIntervals ++ ampIntervals) {
154
155
      val targetName = intervals.bed.getName.stripSuffix(".bed")
      val targetDir = new File(outputDir, targetName)
Peter van 't Hof's avatar
Peter van 't Hof committed
156
157

      val biStrict = BedtoolsIntersect(this, inputBam, intervals.bed,
158
        output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.sam"),
Peter van 't Hof's avatar
Peter van 't Hof committed
159
        minOverlap = config("strict_intersect_overlap", default = 1.0))
160
161
      val biopetFlagstatStrict = BiopetFlagstat(this, biStrict.output, targetDir)
      addSummarizable(biopetFlagstatStrict, targetName + "_biopet_flagstat_strict")
162
      add(new BiopetFifoPipe(this, List(biStrict, biopetFlagstatStrict)))
Peter van 't Hof's avatar
Peter van 't Hof committed
163
164

      val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed,
165
        output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.sam"),
Peter van 't Hof's avatar
Peter van 't Hof committed
166
        minOverlap = config("loose_intersect_overlap", default = 0.01))
167
168
      val biopetFlagstatLoose = BiopetFlagstat(this, biLoose.output, targetDir)
      addSummarizable(biopetFlagstatLoose, targetName + "_biopet_flagstat_loose")
169
      add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))
170

Peter van 't Hof's avatar
Peter van 't Hof committed
171
172
173
174
175
176
177
178
179
      val sortedBed = BamMetrics.sortedbedCache.getOrElse(intervals.bed, {
        val sorter = new BedtoolsSort(this)
        sorter.input = intervals.bed
        sorter.output = swapExt(targetDir, intervals.bed, ".bed", ".sorted.bed")
        add(sorter)
        BamMetrics.sortedbedCache += intervals.bed -> sorter.output
        sorter.output
      })
      val bedCov = BedtoolsCoverage(this, sortedBed, inputBam, depth = true)
180
      val covStats = CoverageStats(this, targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
Peter van 't Hof's avatar
Peter van 't Hof committed
181
182
      covStats.title = Some("Coverage Plot")
      covStats.subTitle = Some(s"for file '$targetName.bed'")
183
      add(bedCov | covStats)
Peter van 't Hof's avatar
Peter van 't Hof committed
184
      addSummarizable(covStats, targetName + "_cov_stats")
185
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
186

Peter van 't Hof's avatar
Peter van 't Hof committed
187
    addSummaryJobs()
188
189
190
191
  }
}

object BamMetrics extends PipelineCommand {
Peter van 't Hof's avatar
Peter van 't Hof committed
192
  /** Make default implementation of BamMetrics and runs script already */
Peter van 't Hof's avatar
Peter van 't Hof committed
193
194
195
196
  def apply(root: Configurable,
            bamFile: File, outputDir: File,
            sampleId: Option[String] = None,
            libId: Option[String] = None): BamMetrics = {
197
    val bamMetrics = new BamMetrics(root)
Peter van 't Hof's avatar
Peter van 't Hof committed
198
199
    bamMetrics.sampleId = sampleId
    bamMetrics.libId = libId
200
201
202
    bamMetrics.inputBam = bamFile
    bamMetrics.outputDir = outputDir

Peter van 't Hof's avatar
Peter van 't Hof committed
203
204
205
    bamMetrics.init()
    bamMetrics.biopetScript()
    bamMetrics
206
  }
Peter van 't Hof's avatar
Peter van 't Hof committed
207
208

  private var sortedbedCache: Map[File, File] = Map()
209
}