Class/Object

dagr.pipelines

DnaResequencingFromFastqPipeline

Related Docs: object DnaResequencingFromFastqPipeline | package pipelines

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class DnaResequencingFromFastqPipeline extends Pipeline

Annotations
@ClpAnnotation()
Linear Supertypes
Pipeline, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. DnaResequencingFromFastqPipeline
  2. Pipeline
  3. LazyLogging
  4. Task
  5. Dependable
  6. AnyRef
  7. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new DnaResequencingFromFastqPipeline(fastq1: List[PathToFastq], fastq2: List[PathToFastq], ref: PathToFasta, sample: String, library: String, platformUnit: List[String], useBwaBacktrack: Boolean = false, numBwaMemThreads: Int = 3, downsampleToReads: Long = Math.round(185e6 / 101), targetIntervals: Option[PathToIntervals], tmp: Path, out: DirPath, basename: Option[FilenamePrefix], qualityFormat: Option[FastqQualityFormat] = None)

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. def !=>(other: Dependable): Unit

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    Definition Classes
    Task → Dependable

  3. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  4. def +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from DnaResequencingFromFastqPipeline to any2stringadd[DnaResequencingFromFastqPipeline] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  5. def ->[B](y: B): (DnaResequencingFromFastqPipeline, B)

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    Implicit information
    This member is added by an implicit conversion from DnaResequencingFromFastqPipeline to ArrowAssoc[DnaResequencingFromFastqPipeline] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()

  6. def ::(other: Option[Dependable]): Dependable

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    Definition Classes
    Dependable

  7. def ::(other: Dependable): Dependable

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    Definition Classes
    Dependable

  8. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  9. final def ==>(other: Option[Dependable]): Dependable

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    Definition Classes
    Dependable

  10. final def ==>(other: Dependable): Dependable

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    Definition Classes
    Dependable

  11. def addDependent(dependent: Dependable): Unit

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    Definition Classes
    Task → Dependable

  12. def allTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  13. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  14. val basename: Option[FilenamePrefix]

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  15. def build(): Unit

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    Main method that constructs all the tasks in the pipeline and wires their dependencies together.

    Main method that constructs all the tasks in the pipeline and wires their dependencies together.

    Definition Classes
    DnaResequencingFromFastqPipeline → Pipeline

  16. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  17. def contains(task: Task): Boolean

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    Definition Classes
    Pipeline

  18. val downsampleToReads: Long

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  19. def ensuring(cond: (DnaResequencingFromFastqPipeline) ⇒ Boolean, msg: ⇒ Any): DnaResequencingFromFastqPipeline

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    Implicit information
    This member is added by an implicit conversion from DnaResequencingFromFastqPipeline to Ensuring[DnaResequencingFromFastqPipeline] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  20. def ensuring(cond: (DnaResequencingFromFastqPipeline) ⇒ Boolean): DnaResequencingFromFastqPipeline

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    Implicit information
    This member is added by an implicit conversion from DnaResequencingFromFastqPipeline to Ensuring[DnaResequencingFromFastqPipeline] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  21. def ensuring(cond: Boolean, msg: ⇒ Any): DnaResequencingFromFastqPipeline

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    Implicit information
    This member is added by an implicit conversion from DnaResequencingFromFastqPipeline to Ensuring[DnaResequencingFromFastqPipeline] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  22. def ensuring(cond: Boolean): DnaResequencingFromFastqPipeline

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    Implicit information
    This member is added by an implicit conversion from DnaResequencingFromFastqPipeline to Ensuring[DnaResequencingFromFastqPipeline] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  23. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  24. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  25. var errors: ListBuffer[String]

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  26. val fastq1: List[PathToFastq]

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  27. val fastq2: List[PathToFastq]

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  28. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  29. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from DnaResequencingFromFastqPipeline to StringFormat[DnaResequencingFromFastqPipeline] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

  30. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  31. final def getTasks: Traversable[_ <: Task]

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    Definition Classes
    Pipeline → Task

  32. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  33. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  34. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  35. val library: String

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  36. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  37. var name: String

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    Definition Classes
    Task

  38. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  39. final def notify(): Unit

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    Definition Classes
    AnyRef

  40. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  41. val numBwaMemThreads: Int

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  42. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  43. val out: DirPath

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  44. val outputDirectory: Option[Path]

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    Definition Classes
    Pipeline

  45. val platformUnit: List[String]

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  46. val qualityFormat: Option[FastqQualityFormat]

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  47. val ref: PathToFasta

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  48. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  49. val root: Dependable

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    Definition Classes
    Pipeline

  50. val sample: String

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  51. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  52. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  53. val targetIntervals: Option[PathToIntervals]

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  54. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  55. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  56. val tmp: Path

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  57. def toString(): String

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    Definition Classes
    AnyRef → Any

  58. val useBwaBacktrack: Boolean

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  59. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  60. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  61. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  62. def withName(name: String): DnaResequencingFromFastqPipeline.this.type

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    Definition Classes
    Task

  63. def →[B](y: B): (DnaResequencingFromFastqPipeline, B)

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    Implicit information
    This member is added by an implicit conversion from DnaResequencingFromFastqPipeline to ArrowAssoc[DnaResequencingFromFastqPipeline] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Pipeline

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from DnaResequencingFromFastqPipeline to any2stringadd[DnaResequencingFromFastqPipeline]

Inherited by implicit conversion StringFormat from DnaResequencingFromFastqPipeline to StringFormat[DnaResequencingFromFastqPipeline]

Inherited by implicit conversion Ensuring from DnaResequencingFromFastqPipeline to Ensuring[DnaResequencingFromFastqPipeline]

Inherited by implicit conversion ArrowAssoc from DnaResequencingFromFastqPipeline to ArrowAssoc[DnaResequencingFromFastqPipeline]

Ungrouped