Class/Object

dagr.tasks.gatk

GatkTask

Related Docs: object GatkTask | package gatk

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abstract class GatkTask extends ProcessTask with JarTask with FixedResources with Configuration

Abstract base class for tasks that involve running the GATK.

Linear Supertypes
Configuration, ConfigurationLike, FixedResources, ScheduleWithEmptyDefaultResources, JarTask, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
Known Subclasses
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. GatkTask
  2. Configuration
  3. ConfigurationLike
  4. FixedResources
  5. ScheduleWithEmptyDefaultResources
  6. JarTask
  7. ProcessTask
  8. UnitTask
  9. Schedulable
  10. LazyLogging
  11. Task
  12. Dependable
  13. AnyRef
  14. 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 GatkTask(walker: String, ref: PathToFasta, intervals: Option[PathToIntervals] = None)

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Abstract Value Members

  1. abstract def addWalkerArgs(buffer: ListBuffer[Any]): Unit

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    Attributes
    protected

Concrete 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 GatkTask to any2stringadd[GatkTask] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  6. def ->[B](y: B): (GatkTask, B)

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    Implicit information
    This member is added by an implicit conversion from GatkTask to ArrowAssoc[GatkTask] 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 applyResources(resources: ResourceSet): Unit

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    Definition Classes
    UnitTask → Schedulable
  12. def args: Seq[Any]

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    Definition Classes
    GatkTask → ProcessTask
  13. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  14. def asType[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Attributes
    protected
    Definition Classes
    ConfigurationLike
  15. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  16. def commandLineName: String

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    Definition Classes
    ConfigurationLike
  17. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike
  18. def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike
  19. def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike
  20. def configureExecutable(path: String, executable: String): Path

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    Definition Classes
    ConfigurationLike
  21. def configureExecutableFromBinDirectory(binPath: String, executable: String): Path

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    Definition Classes
    ConfigurationLike
  22. def ensuring(cond: (GatkTask) ⇒ Boolean, msg: ⇒ Any): GatkTask

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    Implicit information
    This member is added by an implicit conversion from GatkTask to Ensuring[GatkTask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  23. def ensuring(cond: (GatkTask) ⇒ Boolean): GatkTask

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    Implicit information
    This member is added by an implicit conversion from GatkTask to Ensuring[GatkTask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  24. def ensuring(cond: Boolean, msg: ⇒ Any): GatkTask

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    Implicit information
    This member is added by an implicit conversion from GatkTask to Ensuring[GatkTask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  25. def ensuring(cond: Boolean): GatkTask

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    Implicit information
    This member is added by an implicit conversion from GatkTask to Ensuring[GatkTask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  26. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  27. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  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 GatkTask to StringFormat[GatkTask] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  30. def gatkJar: Path

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    Can be overridden to use a specific GATK jar.

    Can be overridden to use a specific GATK jar.

    Attributes
    protected
  31. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  32. final def getTasks: Traversable[_ <: GatkTask.this.type]

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    Definition Classes
    UnitTask → Task
  33. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  34. val intervals: Option[PathToIntervals]

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  35. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  36. def jarArgs(jarPath: Path, jvmArgs: Traversable[String] = Nil, jvmProperties: Map[String, String] = Map.empty, jvmMemory: Memory, useAdvancedGcOptions: Boolean = true): List[String]

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    Attributes
    protected
    Definition Classes
    JarTask
  37. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging
  38. var name: String

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    Definition Classes
    Task
  39. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  40. final def notify(): Unit

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    Definition Classes
    AnyRef
  41. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  42. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task
  43. def optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

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    Definition Classes
    ConfigurationLike
  44. def pickResources(availableResources: ResourceSet): Option[ResourceSet]

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    Definition Classes
    FixedResources → Schedulable
  45. val ref: PathToFasta

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  46. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task
  47. def requires(cores: Double, memory: String): GatkTask.this.type

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    Definition Classes
    FixedResources
  48. def requires(cores: Cores, memory: Memory): GatkTask.this.type

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    Definition Classes
    FixedResources
  49. def requires(resources: ResourceSet): GatkTask.this.type

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    Definition Classes
    FixedResources
  50. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources
  51. def retry(taskInfo: TaskExecutionInfo, failedOnComplete: Boolean): Option[Task]

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    Definition Classes
    Task
  52. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  53. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike
  54. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any
  55. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  56. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  57. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  58. val walker: String

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  59. def withName(name: String): GatkTask.this.type

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    Definition Classes
    Task
  60. def [B](y: B): (GatkTask, B)

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

Inherited from Configuration

Inherited from ConfigurationLike

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from JarTask

Inherited from ProcessTask

Inherited from UnitTask

Inherited from Schedulable

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped