Documentation issues

[illusional]

An issue to keep tabs on documentation, and which things need to be documented:

General

• [ ] Engine comparison
  • Call-caching
  • Debugging
  • Logging
  • Execution environment support
• [ ] Conditionals - relies on PMCC-BioinformaticsCore/janis-core/pull/5
• [ ] WES / TES - How does Janis complement these specifications (notes have been prepared)
• [ ] How to collect outputs in a Tool
• [ ] Collaborations
• [x] Container overrides

Tutorials

• [ ] How to debug Janis + Cromwell
• [ ] Building a WGS pipeline
• [x] Renaming your outputs
  • [ ] How to ensure your output has a specific extension.
• [x] Configuring Janis for HPCs
• [x] How to add and test a tool into the Janis repo

Contributing

• [ ] Contributing Guide
• [ ] Open source comments [SHEP-46]
• [ ] Types of conditionals

Tool registries

• [x] Why it's structured the way it is

Workshops

TBA