[REQUEST] Incorporate Nextclade

[molly-hetheringtonrauth]

Feature Request

We want to incorporate nextclade into the RSV workflow.

Solution

1. we need to update the nextclade json parser python script to inlcude RSV as an organism option.
2. we need to incorporate nextclade into the assembly workflow because, we will need to know the type (A or B) in order to use the correct nextclade dataset. Then we can merge the results in the summary results workflow.

Upstream effects

none.

Downstream effects

none.

[danpolanco]

We are changing directions and getting rid of nextclade_json_parser.py. So instead, we are going to put clade, G_clade, total substitutions, etc in the summary.py.

[molly-hetheringtonrauth]

We will pull the clade, G clade, total substitutions from the nextclade.csv output. We will need to refactor the summary.py script.