BiopetQScript.scala 6.62 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.core

import java.io.File
18

Peter van 't Hof's avatar
Peter van 't Hof committed
19
import nl.lumc.sasc.biopet.core.summary.{SummaryQScript, WriteSummary}
Peter van 't Hof's avatar
Peter van 't Hof committed
20
import nl.lumc.sasc.biopet.utils.config.Configurable
21
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
Peter van 't Hof's avatar
Peter van 't Hof committed
22
import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
Peter van 't Hof's avatar
Peter van 't Hof committed
23
import nl.lumc.sasc.biopet.utils.Logging
Peter van 't Hof's avatar
Peter van 't Hof committed
24
import org.broadinstitute.gatk.queue.{QScript, QSettings}
Peter van 't Hof's avatar
Peter van 't Hof committed
25
import org.broadinstitute.gatk.queue.function.QFunction
Peter van 't Hof's avatar
Peter van 't Hof committed
26
import org.broadinstitute.gatk.queue.util.{Logging => GatkLogging}
27

Peter van 't Hof's avatar
Peter van 't Hof committed
28
/** Base for biopet pipeline */
29
trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
30

31
  @Argument(doc = "JSON / YAML config file(s)", fullName = "config_file", shortName = "config", required = false)
32
  val configfiles: List[File] = Nil
bow's avatar
bow committed
33

Sander Bollen's avatar
Sander Bollen committed
34
  @Argument(doc = "Config values, value should be formatted like 'key=value' or 'namespace:namespace:key=value'", fullName = "config_value", shortName = "cv", required = false)
35
36
  val configValues: List[String] = Nil

Peter van 't Hof's avatar
Peter van 't Hof committed
37
  /** Output directory of pipeline */
Peter van 't Hof's avatar
Peter van 't Hof committed
38
  var outputDir: File = {
Peter van 't Hof's avatar
Peter van 't Hof committed
39
40
    if (config.contains("output_dir", path = Nil)) config("output_dir", path = Nil).asFile
    else new File(".")
41
  }
bow's avatar
bow committed
42

43
  @Argument(doc = "Disable all scatters", shortName = "DSC", required = false)
44
  var disableScatter: Boolean = false
45

bow's avatar
bow committed
46
47
  var outputFiles: Map[String, File] = Map()

Peter van 't Hof's avatar
Peter van 't Hof committed
48
  type InputFile = BiopetQScript.InputFile
49
50
51

  var inputFiles: List[InputFile] = Nil

Peter van 't Hof's avatar
Peter van 't Hof committed
52
  /** Get implemented from org.broadinstitute.gatk.queue.QScript */
Peter van 't Hof's avatar
Peter van 't Hof committed
53
  var qSettings: QSettings
bow's avatar
bow committed
54

Peter van 't Hof's avatar
Peter van 't Hof committed
55
56
57
58
  /** Get implemented from org.broadinstitute.gatk.queue.QScript */
  var functions: Seq[QFunction]

  /** Init for pipeline */
59
  def init()
bow's avatar
bow committed
60

Peter van 't Hof's avatar
Peter van 't Hof committed
61
  /** Pipeline itself */
62
  def biopetScript()
Peter van 't Hof's avatar
Peter van 't Hof committed
63

64
65
66
  /** Returns the extension to make the report */
  def reportClass: Option[ReportBuilderExtension] = None

67
68
  val skipWriteDependencies: Boolean = config("skip_write_dependencies", default = false)

Peter van 't Hof's avatar
Peter van 't Hof committed
69
  /** Script from queue itself, final to force some checks for each pipeline and write report */
70
  final def script() {
Peter van 't Hof's avatar
Peter van 't Hof committed
71
72
    outputDir = config("output_dir")
    outputDir = outputDir.getAbsoluteFile
73
74
75

    BiopetQScript.checkOutputDir(outputDir)

76
77
    init()
    biopetScript()
Peter van 't Hof's avatar
Peter van 't Hof committed
78
    logger.info("Biopet script done")
79

Peter van 't Hof's avatar
Peter van 't Hof committed
80
81
82
83
84
85
    if (disableScatter) {
      logger.info("Disable scatters")
      for (function <- functions) function match {
        case f: ScatterGatherableFunction => f.scatterCount = 1
        case _                            =>
      }
86
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
87
88
89
90

    this match {
      case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
        logger.info("Write report is skipped because sample flag is used")
91
92
93
      case _ => reportClass.foreach { report =>
        add(report)
      }
Peter van 't Hof's avatar
Peter van 't Hof committed
94
95
    }

Peter van 't Hof's avatar
Peter van 't Hof committed
96
    logger.info("Running pre commands")
97
    for (function <- functions) function match {
98
      case f: BiopetCommandLineFunction =>
99
100
        f.preProcessExecutable()
        f.beforeGraph()
Peter van 't Hof's avatar
Peter van 't Hof committed
101
        f.internalBeforeGraph()
Peter van 't Hof's avatar
Peter van 't Hof committed
102
        f.commandLine
Peter van 't Hof's avatar
Peter van 't Hof committed
103
104
      case f: WriteSummary => f.init()
      case _               =>
105
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
106

Peter van 't Hof's avatar
Peter van 't Hof committed
107
108
    if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
      globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
Sander Bollen's avatar
Sander Bollen committed
109
    else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, output directory cannot be created")
110

Peter van 't Hof's avatar
Peter van 't Hof committed
111
112
    logger.info("Checking input files")
    inputFiles.par.foreach { i =>
Peter van 't Hof's avatar
Peter van 't Hof committed
113
      if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
114
      if (!i.file.canRead) Logging.addError(s"Input file can not be read: ${i.file}")
Sander Bollen's avatar
Sander Bollen committed
115
      if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absolute path: ${i.file}")
116
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
117

Peter van 't Hof's avatar
Peter van 't Hof committed
118
    functions.filter(_.jobOutputFile == null).foreach(f => {
Peter van 't Hof's avatar
Peter van 't Hof committed
119
      try {
Peter van 't Hof's avatar
Peter van 't Hof committed
120
121
        val className = if (f.getClass.isAnonymousClass) f.getClass.getSuperclass.getSimpleName else f.getClass.getSimpleName
        f.jobOutputFile = new File(f.firstOutput.getAbsoluteFile.getParent, "." + f.firstOutput.getName + "." + className + ".out")
Peter van 't Hof's avatar
Peter van 't Hof committed
122
123
124
      } catch {
        case e: NullPointerException => logger.warn(s"Can't generate a jobOutputFile for $f")
      }
Peter van 't Hof's avatar
Peter van 't Hof committed
125
    })
126

Peter van 't Hof's avatar
Peter van 't Hof committed
127
128
129
    if (!skipWriteDependencies) WriteDependencies.writeDependencies(
      functions,
      new File(outputDir, ".log" + File.separator + BiopetQCommandLine.timestamp + File.separator + "graph"))
130

Peter van 't Hof's avatar
Peter van 't Hof committed
131
    Logging.checkErrors()
Peter van 't Hof's avatar
Peter van 't Hof committed
132
    logger.info("Script complete without errors")
133
  }
bow's avatar
bow committed
134

Peter van 't Hof's avatar
Peter van 't Hof committed
135
136
137
  /** Get implemented from org.broadinstitute.gatk.queue.QScript */
  def add(functions: QFunction*)

138
  /** Get implemented from org.broadinstitute.gatk.queue.QScript */
Peter van 't Hof's avatar
Peter van 't Hof committed
139
  def addAll(functions: scala.Traversable[org.broadinstitute.gatk.queue.function.QFunction])
140

141
  /** Function to set isIntermediate and add in 1 line */
bow's avatar
bow committed
142
  def add(function: QFunction, isIntermediate: Boolean = false) {
143
144
145
    function.isIntermediate = isIntermediate
    add(function)
  }
146
147
148
149
150
151
152
153
154

  def add(subPipeline: QScript): Unit = {
    subPipeline.qSettings = this.qSettings
    subPipeline match {
      case that: SummaryQScript =>
        that.init()
        that.biopetScript()
        this match {
          case s: SummaryQScript => s.addSummaryQScript(that)
Peter van 't Hof's avatar
Peter van 't Hof committed
155
          case _                 =>
156
        }
Peter van 't Hof's avatar
Peter van 't Hof committed
157
      case that: BiopetQScript =>
158
159
160
161
162
163
        that.init()
        that.biopetScript()
      case _ => subPipeline.script
    }
    addAll(subPipeline.functions)
  }
164
}
Peter van 't Hof's avatar
Peter van 't Hof committed
165
166

object BiopetQScript {
Peter van 't Hof's avatar
Peter van 't Hof committed
167
  case class InputFile(file: File, md5: Option[String] = None)
168
169
170

  def checkOutputDir(outputDir: File): Unit = {
    // Sanity checks
Peter van 't Hof's avatar
Peter van 't Hof committed
171
172
    require(outputDir.getAbsoluteFile.getParentFile.canRead, s"No premision to read parent of outputdir: ${outputDir.getParentFile}")
    require(outputDir.getAbsoluteFile.getParentFile.canWrite, s"No premision to write parent of outputdir: ${outputDir.getParentFile}")
173
    outputDir.mkdir()
Peter van 't Hof's avatar
Peter van 't Hof committed
174
175
    require(outputDir.getAbsoluteFile.canRead, s"No premision to read outputdir: $outputDir")
    require(outputDir.getAbsoluteFile.canWrite, s"No premision to write outputdir: $outputDir")
176
  }
Peter van 't Hof's avatar
Peter van 't Hof committed
177
178


179
}