Improve the documentation of Dagr

[nh13]

Given the impending merge of a new execution system and support for replays, I would like to collate a list of documentation that needs to be created. Please edit this comment with any agreed upon changes.

• Main page (location example: https://fulcrumgenomics.github.io/dagr)
  • 2-3 sentence description
  • 3-4 core features (why dage?)
  • where to get started (download and run example)
  • links to key documentation, source code, issue tracking, and support
• Documentation
  • Quick Start for users
    • Requirements
    • Installation
    • Hello World
    • A more complicated example (ex. SleepyPipeline)
  • Running Dagr
    • Command line options
    • Configuration
      • Config File
      • Resources (Cores & Memory)
    • Scripts and Logs
    • Execution status
      • Interactive Mode
      • Execution Report
    • Replay
    • Experimental Execution
  • For Pipeline Authors
    • Tasks and Dependencies
      • Task
      • Dependencies AKA ==>
      • Task Groups AKA ::
      • UnitTask
      • Pipelines AKA Pipeline and root
      • When Tasks are Built AKA getTasks
    • Core Tasks
      • Tasks in the Shell: ProcessTask
        • ShellCommand
      • InJvmTask and SimpleInJvmTask
      • Pipe
        • Pipe, PipeIn, PipeOut
      • Linker
      • NoOpTask and NoOpInJvmTask
      • EitherTask
      • Links to bioinformatics tasks (ex. PicardTask, FgbioTask, Bwa) [we should make docs for these too!]
    • Scheduling and Execution
      • How it works
      • Which Execution Systems (aka single compute)
    • Resources
      • Cores
      • Memory
      • Picking Resources (when, how)
      • FixedResoures and Variable Resources
    • Retry
      • Retrying a number of times: MultipleRetry
      • Retrying with More Memory: MemoryRetry, LinearyMemoryRetry, and MemoryDoublingRetry
      • JvmRanOutOfMemory
    • Common Patterns
    • Bioinformatcs Tasks (split off dagr-tasks)
    • Contributing to Dagr
  • Examples
    • Link to Projects Using Dagr
    • Some Example Bioinformatic Pipelines (split off `dagr-pipelines)