Welcome to WfExS-backend’s documentation!

WfExS-backend (/why’fex/) is a high-level workflow orchestrator designed for reproducible and secure workflow executions in isolated environments, promoting analysis reproducibility and replicability using potentially sensitive data. Mainly, WfExS is used to import and execute workflows.

Note

This project is under active development.

Content

• 🚀 Getting Started
  • System requirements
  • Core dependencies
  • Additional Software Dependencies
    • Installation
    • Easy creation of WfExS container image
    • Gearshift specific installation instructions
• 📄 Configuration
  • Local configuration
    • Main local configuration parameters
  • Workflow staging configuration
  • Security contexts file
• ⚙️ Executing WfExS
  • Testing the Software: Running a Test Workflow
  • Working with WfExS to Run Your Own Workflow
• How to Contribute
• General Websites
• Available features
  • Workflow Engines
  • Containers
  • Export Plugins
  • Fetchers
  • Licences
• Command-line description
• CLI directives
  • Named Arguments
  • commands
  • Sub-commands
    • init
    • populate-side-caches
    • cache
    • staged-workdir
    • export
    • list-fetchers
    • list-exporters
    • list-container-factories
    • list-workflow-engines
    • list-licences
    • config-validate
    • stage
    • re-stage
    • import
    • mount-workdir
    • export-stage
    • offline-execute
    • execute
    • export-results
    • export-crate
• JSON Schema Reference
  • WfExS-backend cache metadata
    • 1. Property WfExS-backend cache metadata > oneOf > item 0
    • 2. Property WfExS-backend cache metadata > oneOf > item 1
    • 3. Property WfExS-backend cache metadata > stamp
    • 4. Property WfExS-backend cache metadata > licences
    • 5. Property WfExS-backend cache metadata > metadata_array
  • WfExS-backend exports definition
    • 1. Property WfExS-backend exports definition > exports
  • WfExS-backend config
    • 1. Property WfExS-backend config > cacheDir
    • 2. Property WfExS-backend config > crypt4gh
    • 3. Property WfExS-backend config > tools
    • 4. Property WfExS-backend config > workDir
    • 5. Property WfExS-backend config > fetchers-setup
  • WfExS-backend stage definition
    • 1. Property WfExS-backend stage definition > trs_endpoint
    • 2. Property WfExS-backend stage definition > version
    • 3. Property WfExS-backend stage definition > workflow_id
    • 4. Property WfExS-backend stage definition > nickname
    • 5. Property WfExS-backend stage definition > paranoid_mode
    • 6. Property WfExS-backend stage definition > workflow_type
    • 7. Property WfExS-backend stage definition > workflow_config
    • 8. Property WfExS-backend stage definition > placeholders
    • 9. Property WfExS-backend stage definition > params
    • 10. Property WfExS-backend stage definition > profile
    • 11. Property WfExS-backend stage definition > environment
    • 12. Property WfExS-backend stage definition > outputs
    • 13. Property WfExS-backend stage definition > default_actions
  • WfExS-backend security context
    • 1. Pattern Property WfExS-backend security context > Security context by name
    • 2. Pattern Property WfExS-backend security context > Security context by prefix
• API Reference
  • wfexs_backend
    • Subpackages
    • Submodules
    • Package Contents