Class/Object

dagr.pipelines

CreateUnmappedBamFromFastqPipeline

Related Docs: object CreateUnmappedBamFromFastqPipeline | package pipelines

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class CreateUnmappedBamFromFastqPipeline extends Pipeline

Annotations
@ClpAnnotation()
Linear Supertypes
Pipeline, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. CreateUnmappedBamFromFastqPipeline
  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 CreateUnmappedBamFromFastqPipeline(fastq1: List[PathToFastq], fastq2: List[PathToFastq], ref: PathToFasta, sample: String, library: String, platformUnit: List[String], tmp: Path, out: DirPath, basename: Option[FilenamePrefix] = None, unmappedBam: Option[PathToBam] = None)

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Value Members

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

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    Definition Classes
    AnyRef → Any

  2. def !=>(other: MultiTask): other.type

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    Definition Classes
    Task → Dependable

  3. def !=>(other: Task): other.type

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    Definition Classes
    Task → Dependable

  4. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  5. def +(other: String): String

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

  6. def ->[B](y: B): (CreateUnmappedBamFromFastqPipeline, B)

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

  7. def ::(other: Task): MultiTask

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef → Any

  9. def ==>(other: MultiTask): other.type

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    Definition Classes
    Task → Dependable

  10. def ==>(other: Task): other.type

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    Definition Classes
    Task → Dependable

  11. def addTask(task: Task): task.type

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    Definition Classes
    Pipeline

  12. def addTasks(task: Task*): Unit

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    Definition Classes
    Pipeline

  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
    CreateUnmappedBamFromFastqPipeline → 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. def ensuring(cond: (CreateUnmappedBamFromFastqPipeline) ⇒ Boolean, msg: ⇒ Any): CreateUnmappedBamFromFastqPipeline

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

  19. def ensuring(cond: (CreateUnmappedBamFromFastqPipeline) ⇒ Boolean): CreateUnmappedBamFromFastqPipeline

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

  20. def ensuring(cond: Boolean, msg: ⇒ Any): CreateUnmappedBamFromFastqPipeline

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

  21. def ensuring(cond: Boolean): CreateUnmappedBamFromFastqPipeline

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

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

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    Definition Classes
    AnyRef

  23. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  24. var errors: ListBuffer[String]

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  25. val fastq1: List[PathToFastq]

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  26. val fastq2: List[PathToFastq]

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  27. def finalize(): Unit

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

  28. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    Pipeline → Task

  31. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  32. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  33. val library: String

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  34. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  35. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  37. final def notify(): Unit

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    Definition Classes
    AnyRef

  38. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  39. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  40. val out: DirPath

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  41. val outputDirectory: Option[Path]

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    Definition Classes
    Pipeline

  42. val platformUnit: List[String]

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  43. val ref: PathToFasta

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  44. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  45. def retry(taskInfo: TaskExecutionInfo, failedOnComplete: Boolean): Option[Task]

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    Definition Classes
    Task

  46. val root: Dependable

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    Definition Classes
    Pipeline

  47. val sample: String

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

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    Definition Classes
    AnyRef

  49. val tmp: Path

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  50. def toString(): String

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    Definition Classes
    AnyRef → Any

  51. var unmappedBam: Option[PathToBam]

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  52. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  55. def withName(name: String): CreateUnmappedBamFromFastqPipeline.this.type

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    Definition Classes
    Task

  56. def →[B](y: B): (CreateUnmappedBamFromFastqPipeline, B)

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    Implicit information
    This member is added by an implicit conversion from CreateUnmappedBamFromFastqPipeline to ArrowAssoc[CreateUnmappedBamFromFastqPipeline] 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 CreateUnmappedBamFromFastqPipeline to any2stringadd[CreateUnmappedBamFromFastqPipeline]

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

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

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

Ungrouped