Update nextclade to version to 3.9.0

[bwlang]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[bwlang]

@pvanheus
I thought this might be a simple upgrade to a new tool version... but it seems not.
Looks like this was mostly your work - want to to collaborate a bit on the update? ( I want RSV features...)

[pvanheus]

@pvanheus I thought this might be a simple upgrade to a new tool version... but it seems not. Looks like this was mostly your work - want to to collaborate a bit on the update? ( I want RSV features...)

Sure. One problem with the current wrapper though, is related to how Galaxy handles column metadata: this is a static list, whereas in Nextclade the output columns change dependent on what dataset you're using. So this means that the column headers have to be included in the Nextclade output because Galaxy's metadata-based column headers don't work. Which is annoying if you want to be able to concatenate Nextclade results together.