MultiSampleQScript.scala 6.52 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
/**
 * 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.
 */
16
17
package nl.lumc.sasc.biopet.core

18
19
import java.io.File

Peter van 't Hof's avatar
Peter van 't Hof committed
20
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
Peter van 't Hof's avatar
Peter van 't Hof committed
21
import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
22
import org.broadinstitute.gatk.queue.QScript
23
import org.broadinstitute.gatk.utils.commandline.Argument
24

Peter van 't Hof's avatar
Peter van 't Hof committed
25
/** This trait creates a structured way of use multisample pipelines */
26
trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
27

28
  @Argument(doc = "Only Sample", shortName = "s", required = false, fullName = "sample")
29
  private[core] val onlySamples: List[String] = Nil
Peter van 't Hof's avatar
Peter van 't Hof committed
30

31
  require(globalConfig.map.contains("samples"), "No Samples found in config")
Peter van 't Hof's avatar
Peter van 't Hof committed
32

Peter van 't Hof's avatar
Peter van 't Hof committed
33
  /** Sample class with basic functions build in */
34
  abstract class AbstractSample(val sampleId: String) extends Summarizable {
Peter van 't Hof's avatar
Peter van 't Hof committed
35
    /** Overrules config of qscript with default sample */
Peter van 't Hof's avatar
Peter van 't Hof committed
36
    val config = new ConfigFunctions(defaultSample = sampleId)
Peter van 't Hof's avatar
Peter van 't Hof committed
37

38
39
40
    /** Sample specific settings */
    def summarySettings: Map[String, Any] = Map()

Peter van 't Hof's avatar
Peter van 't Hof committed
41
    /** Library class with basic functions build in */
42
    abstract class AbstractLibrary(val libId: String) extends Summarizable {
Peter van 't Hof's avatar
Peter van 't Hof committed
43
      /** Overrules config of qscript with default sample and default library */
44
      val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
45

Peter van 't Hof's avatar
Peter van 't Hof committed
46
      /** Name overules the one from qscript */
47
48
49
50
      def addSummarizable(summarizable: Summarizable, name: String): Unit = {
        qscript.addSummarizable(summarizable, name, Some(sampleId), Some(libId))
      }

51
52
53
      /** Library specific settings */
      def summarySettings: Map[String, Any] = Map()

Peter van 't Hof's avatar
Peter van 't Hof committed
54
      /** Adds the library jobs */
Peter van 't Hof's avatar
Peter van 't Hof committed
55
      final def addAndTrackJobs(): Unit = {
Peter van 't Hof's avatar
Peter van 't Hof committed
56
        if (nameRegex.findFirstIn(libId) == None)
Peter van 't Hof's avatar
Peter van 't Hof committed
57
          Logging.addError(s"Library '$libId' $nameError")
58
        currentSample = Some(sampleId)
59
        currentLib = Some(libId)
Peter van 't Hof's avatar
Peter van 't Hof committed
60
        addJobs()
61
        qscript.addSummarizable(this, "pipeline", Some(sampleId), Some(libId))
Peter van 't Hof's avatar
Peter van 't Hof committed
62
        currentLib = None
63
64
65
        currentSample = None
      }

Peter van 't Hof's avatar
Peter van 't Hof committed
66
      /** Creates a library file with given suffix */
67
      def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libId + suffix)
Peter van 't Hof's avatar
Peter van 't Hof committed
68
69

      /** Returns library directory */
Peter van 't Hof's avatar
Peter van 't Hof committed
70
      def libDir = new File(sampleDir, "lib_" + libId)
71

Peter van 't Hof's avatar
Peter van 't Hof committed
72
      /** Function that add library jobs */
Peter van 't Hof's avatar
Peter van 't Hof committed
73
      protected def addJobs()
74
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
75

Peter van 't Hof's avatar
Peter van 't Hof committed
76
    /** Library type, need implementation in pipeline */
77
    type Library <: AbstractLibrary
Peter van 't Hof's avatar
Peter van 't Hof committed
78

Peter van 't Hof's avatar
Peter van 't Hof committed
79
80
    /** Stores all libraries */
    val libraries: Map[String, Library] = libIds.map(id => id -> makeLibrary(id)).toMap
81

Peter van 't Hof's avatar
Peter van 't Hof committed
82
83
84
85
86
    /**
     * Factory method for Library class
     * @param id SampleId
     * @return Sample class
     */
Peter van 't Hof's avatar
Peter van 't Hof committed
87
    def makeLibrary(id: String): Library
Peter van 't Hof's avatar
Peter van 't Hof committed
88

Peter van 't Hof's avatar
Peter van 't Hof committed
89
90
    /** returns a set with library names */
    protected def libIds: Set[String] = {
91
      ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
92
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
93

Peter van 't Hof's avatar
Peter van 't Hof committed
94
    /** Name overules the one from qscript */
95
96
97
98
    def addSummarizable(summarizable: Summarizable, name: String): Unit = {
      qscript.addSummarizable(summarizable, name, Some(sampleId))
    }

Peter van 't Hof's avatar
Peter van 't Hof committed
99
    /** Adds sample jobs */
Peter van 't Hof's avatar
Peter van 't Hof committed
100
    final def addAndTrackJobs(): Unit = {
Peter van 't Hof's avatar
Peter van 't Hof committed
101
      if (nameRegex.findFirstIn(sampleId) == None)
Peter van 't Hof's avatar
Peter van 't Hof committed
102
        Logging.addError(s"Sample '$sampleId' $nameError")
103
      currentSample = Some(sampleId)
Peter van 't Hof's avatar
Peter van 't Hof committed
104
      addJobs()
105
      qscript.addSummarizable(this, "pipeline", Some(sampleId))
106
107
      currentSample = None
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
108

Peter van 't Hof's avatar
Peter van 't Hof committed
109
    /** Function to add sample jobs */
Peter van 't Hof's avatar
Peter van 't Hof committed
110
    protected def addJobs()
Peter van 't Hof's avatar
Peter van 't Hof committed
111

Peter van 't Hof's avatar
Peter van 't Hof committed
112
    /** function add all libraries in one call */
113
    protected final def addPerLibJobs(): Unit = {
114
      for ((libId, library) <- libraries) {
Peter van 't Hof's avatar
Peter van 't Hof committed
115
        library.addAndTrackJobs()
116
      }
bow's avatar
bow committed
117
118
    }

119
    /** Creates a sample file with given suffix */
Peter van 't Hof's avatar
Peter van 't Hof committed
120
121
122
    def createFile(suffix: String) = new File(sampleDir, sampleId + suffix)

    /** Returns sample directory */
Peter van 't Hof's avatar
Peter van 't Hof committed
123
    def sampleDir = new File(outputDir, "samples" + File.separator + sampleId)
124
125
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
126
  /** Sample type, need implementation in pipeline */
Peter van 't Hof's avatar
Peter van 't Hof committed
127
128
  type Sample <: AbstractSample

Peter van 't Hof's avatar
Peter van 't Hof committed
129
130
  /**
   * Factory method for Sample class
131
   * @param id SampleId
Peter van 't Hof's avatar
Peter van 't Hof committed
132
133
   * @return Sample class
   */
134
  def makeSample(id: String): Sample
Peter van 't Hof's avatar
Peter van 't Hof committed
135

Peter van 't Hof's avatar
Peter van 't Hof committed
136
137
  /** Stores all samples */
  val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
138

139
  /** Returns a list of all sampleIDs */
140
  protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
141

Peter van 't Hof's avatar
Peter van 't Hof committed
142
  protected lazy val nameRegex = """^[a-zA-Z0-9][a-zA-Z0-9-_]+[a-zA-Z0-9]$""".r
Peter van 't Hof's avatar
Peter van 't Hof committed
143
144
145
146
  protected lazy val nameError = " name invalid." +
    "Name must have at least 3 characters," +
    "must begin and end with an alphanumeric character, " +
    "and must not have whitespace."
Peter van 't Hof's avatar
Peter van 't Hof committed
147

Peter van 't Hof's avatar
Peter van 't Hof committed
148
  /** Runs addAndTrackJobs method for each sample */
Peter van 't Hof's avatar
Peter van 't Hof committed
149
  final def addSamplesJobs() {
150
    if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {
151
152
153
      samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
      addMultiSampleJobs()
    } else onlySamples.foreach(sampleId => samples.get(sampleId) match {
154
155
156
      case Some(sample) => sample.addAndTrackJobs()
      case None         => logger.warn("sampleId '" + sampleId + "' not found")
    })
157
158
  }

159
  /**
Peter van 't Hof's avatar
Peter van 't Hof committed
160
   * Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
161
162
163
   */
  def addMultiSampleJobs()

Peter van 't Hof's avatar
Peter van 't Hof committed
164
  /** Stores sample state */
165
166
  private var currentSample: Option[String] = None

Peter van 't Hof's avatar
Peter van 't Hof committed
167
168
169
170
  /** Stores library state */
  private var currentLib: Option[String] = None

  /** Prefix full path with sample and library for jobs that's are created in current state */
171
  override def configFullPath: List[String] = {
172
    val sample = currentSample match {
Peter van 't Hof's avatar
Peter van 't Hof committed
173
174
175
      case Some(s) => "samples" :: s :: Nil
      case _       => Nil
    }
176
    val lib = currentLib match {
Peter van 't Hof's avatar
Peter van 't Hof committed
177
178
179
      case Some(l) => "libraries" :: l :: Nil
      case _       => Nil
    }
180
    sample ::: lib ::: super.configFullPath
181
  }
182
}