Integrate Kaiko into WDL pipeline

[ssarrafan]

Kaiko will be integrated into the metaproteomics WDL pipeline.

TODO

• Determine fixed and variable input elements that will need to be captured in input.json
• Investigate GFF or GFF-like file Generation for Kaiko #59
• Implement Annotations File Generation #60
• Expose Kaikos Static Files to Its Container Via Cromwell Config  #61
• Kaiko WDL file #62
• Wire Kaiko into metaproteomics pipeline

[picowatt]

There's an issue with how we're going to expose the static Kaiko files with the Kaiko container. Alicia pointed me towards a mechanism for doing just that by altering the Cromwell config, but this may require some changes to how Kaiko locates files needed during runtime.

[ssarrafan]

Moving to the next sprint per the last comment and the unchecked boxes above.

[ssarrafan]

@picowatt @pdpiehowski @CamiloPosso is this still active?

[pdpiehowski]

Yes, this issue overlapped somewhat with a backlogged issue, and so I closed that one to clean things up a bit.

[ssarrafan]

Not updated in the last 2 weeks. Removing from sprint and adding backlog label.