GeneFlow Tutorials

The following tutorials provide detailed examples for creating and running GeneFlow workflows, apps, and containers.

• Basic App: Hello World
  • Configure the Environment
  • Clone the GeneFlow App Template
  • Define the App
  • “Make” the App
  • Test the App
  • Update the App README
  • Commit the App to a Git Repo
  • Summary
• One-Step Workflow: Hello World
  • Clone the GeneFlow Workflow Template
  • Configure the Workflow
  • Add Test Data
  • Update the Workflow README
  • Commit the Workflow to a Git Repo
  • Install the Workflow from a Git Repo
  • Test the Workflow
  • Summary
• Basic Workflow and App Inputs
  • Modify the “Hello World!” App
  • Modify the “Hello World!” Workflow
  • Summary
• Piped Execution in Apps
  • Modify the “Hello World!” App
  • Modify the “Hello World!” Workflow
  • Summary
• Conditional Execution in Apps
  • Modify the “Hello World!” App
  • Modify the “Hello World!” Workflow
  • Summary
• Multi-Step Workflow
  • The “wc” app
  • Hello World output is the wc input
  • Update the workflow.yaml file
  • Summary
• Advanced Workflow and App Inputs
• Branching Workflow
• Executing Containers in Apps
  • Clone the GeneFlow App Template
  • Configure the App
  • Inputs and Parameters
  • App Execution Methods
  • “Make” the App
  • Test the App
  • Update your README.rst
  • Upload your app
  • Summary
• Build a Container for an App
  • Singularity Requirement
  • A Container for RNA-Seq
  • Singularity Recipe
  • Base Container
  • Copy Files
  • Set Environmental Variables
  • Metadata
  • Install your software
  • Container as an Executable
  • Build your image
  • Working with your image
  • Summary
• Tapis Workflow Installation and Execution