Product backlog

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

2. Extended and completed VRTrack DataSource:
    2b. Method to get lane fastqs with metadata
    2c. Investigate if other methods are needed
        2c.1. Implement other methods

3. Design a generic (DataSource-like?) DataSink API allowing a Step to output results to an arbitrary database table
    3a. Create a new VRPipe Persistent class as an example/default output table
    3b. Should be able to output to VRTrack as well

4. Investigate need for iRods DataSource

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
        5f.2. QC stats & graphs step (that generically works on genome & exome bams?)
    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
    5j. Design a generic system equivalent of the StoreLane/Path pipelines, but that works on all pipeline outputs and isn't necessarily a "pipeline" a user sets up, but a daemon that acts based on low disc space
    5k. Investigate need for import (bam/fasta from file/iRods) pipelines?

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
    13a. Resolve issues with indexing
    13b. Resolve issues with column types
    13c. Get it working fully on Postgres

14. Write & publish paper