fulcrumgenomics/dagr

Improve the documentation of Dagr

nh13 opened this issue · 0 comments

nh13 commented

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)