User Guide

Table of Contents

  1. Introduction
  2. Installation
    1. Requirements
    2. Downloading
    3. Setup and launching
  3. Interface overview
    1. Server library
    2. Personal library
    3. Workflow area
    4. Connection manager
    5. Provenance editor
    6. Preferences
    7. Search feature
    8. Checking for latest updates
    9. Starting GUI from command line
    10. Running from the command line
      1. Submitting workflows from command line
      2. Managing workflows from command line
  4. Building a workflow
    1. Dragging in modules
    2. Connecting modules
      1. Smartline
    3. Setting parameter values
    4. Data sources and data sinks
    5. Cloud sources and cloud sinks
    6. Study module
      1. Input data tab
      2. Grouping tab
      3. Matrix tab
    7. Conditionals
      1. File conditions example
      2. Arithmetical/Comparison example
      3. Metadata conditions example
    8. Web service modules
    9. Transformer modules
    10. Remote file browser
    11. Processing multiple inputs
    12. Enable/Disable parameters
    13. Annotations
    14. Variables
    15. IDA
    16. NDAR
    17. XNAT
    18. Cloud storage
    19. Server changer
  5. Execution
    1. Validation
    2. Executing a workflow
    3. Client disconnect/reconnect
    4. Server status
    5. Pausing a workflow
    6. Stopping a workflow
    7. Restart a module
    8. Module statuses
    9. Viewing output
    10. Debugging execution
    11. Report a bug
  6. Creating modules
    1. Module definition
      1. Info tab
        1. General module information
        2. Citation information
      2. Parameters tab
        1. General parameter information
        2. Parameter types
        3. File types
        4. Parameter arguments size
        5. Advanced parameter information
          1. Select dependencies
          2. Transformations
          3. Output/Error stream extraction
          4. Metadata extraction
          5. Output list file
      3. Execution tab
        1. Executable location
        2. Advanced options
      4. Metadata tab – Metadata Augmentation
    2. Alternative methods
      1. From help file
      2. Module Suggest
    3. Module groups
  7. Advanced Topics
    1. Syncing Execution Flow
    2. Exporting Pipeline Workflow to Script
    3. Remote GUI Invocation
    4. Workflow Diff Utility

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