Lightning

Creation of the CGF files for the 433 1kg and 174+ PGP samples need more resources than a local machine. This will need to scaled up and should use Arvados.

There should be a base of a CGF creation pipeline. This will be used to create the crunch scripts for use on Arvados. This includes working through Arvados issues to push the crunch scripts through to completion as well as working through bugs and issues with the CGF creation.

Completed:

• Underlying data: https://workbench.su92l.arvadosapi.com/projects/su92l-j7d0g-2hk0kr9bayye8n0#Data_collections
• Specification and documentation: https://github.com/abeconnelly/l7g
• Proxy sever: https://github.com/abeconnelly/lci
• Tile Server: https://github.com/abeconnelly/glfd
• CGF tools and server: https://github.com/abeconnelly/cgf
• Phenotype server (untap): https://github.com/abeconnelly/l7g-p7e-untap
• Variant server (ClinVar): https://github.com/abeconnelly/l7g-v5t-clinvar
• Prototype Docker image: https://hub.docker.com/r/abeconnelly/lightning/

There still needs to be an Arvados pipeline for the creation of underlying data but that can be moved to a future ticket.