Image Portal Workflows’s documentation

Image Analysis Workflows, servicing NIAID’s “Hedwig” project.

Please see our Spinx Docs for details.

Contents:

• Project Development
  • Virtual environment Set-up
  • Ancillary utils and .env file
  • Docker and .env file
  • Testing
  • Contributing and GitHub
  • Sphinx Documentation
  • Register Workflows:
  • Git LFS
• Workflows
  • BRT Workflow
  • Spatialomics Workflow
• Submitting Jobs
  • Pipeline Parameters
  • Pipeline Response
  • CLI/SDK Submission
  • Manual Submission
• API
  • em_workflows
• RML HPC (Big Sky)
  • Python environments
  • NFS Filesystem layout
  • Spack
• Managing Prefect Server
  • Continuous Deployment (dev to qa to prod)
• Managing Prefect Worker
  • Deploying workflows
  • Troubleshooting: