Product backlog

Here is a list of VRPipe features that need to be implemented, highest priority first.

5. Convert over remaining VertRes pipelines to VRPipe:
    5b. Merge-across pipeline
    5d. Dindel pipeline
        5d.1. Investigate latest Dindel to work out required steps
    5f. QC pipeline
        5f.1. Genotype checking step
    5g. SV calling pipeline
        5g.1. Investigate steps needed; avoid use of other pipeline systems
    5h. TE calling pipeline
        5h.1. Investigate steps needed
    5i. RNA-seq & Chip-seq pipelines
        5i.1. Investigate steps needed

6. Cmd-line interface to create new Steps and Pipelines

8. Convert trigger and dispatch scripts into daemons
    8a. Trigger daemon should spawn independent daemons for each PipelineSetup
    8b. Another monitor daemon should make sure the trigger and dispatch daemons are running, and vice versa
    8c. Daemons should send emails out on success and failures

9. Add POD documentation for all code

10. Web interface:
    10a. It's own in-built web server daemon
    10b. Ajax-tacular
    10c. Does all the things the cmd-line interfaces can do, but more pretty

11. Create friendly usage guides and intro here on the wiki

12. Complete DRM independence
    12a. Resolve issues with parsing DRM output and resolving back to standard keywords

13. Complete DB independence
    13c. Get it working fully on Postgres

16. Support for submitting to multiple farms (of different types even, eg. cloud)

14. Write & publish paper