Update to Nextclade v3 and deprecate parser

[molly-hetheringtonrauth]

Feature Request

We want to switch over from nextclade 2 to nextclade v3.

Solution

1. re-factor the nextclade json parser script to accomodate the new json format.
2. update the wdl to accommodate the additional nextclade outputs (in nextclade 3, the SARS-CoV-2 genome is split into 2 datasets - ORFs and genes, so we get double the output files).

Upstream effects

none

Downstream effects

the nextclade json parser script will be applied to the influenza and rsv workflow, so we will eventually want to include flags to handle those organisms. The nextclade json parser script will then be placed in a new repo - pipeline_tools.

[molly-hetheringtonrauth]

We want to use the "nextstrain/sars-cov-2/wuhan-hu-1/proteins" dataset.

[molly-hetheringtonrauth]

linked #39