Add Scorpio + constellations column and versions

[RaverJay]

• implements #173
• will add a Scorpio column to the report if any samples had a scorpio call, omitted otherwise
• Scorpio and constellations version is determined by spinning up the pangolin container once

Bonus:

• adds gzip input capabilities for --fasta (e.g. blabla.fasta.gz)
• bumps up default version of Pangolin and Nextclade to new ones

Needs testing

[hoelzer]

great thx @RaverJay !

Just did a test run (that has no Omicron included). But no scorpio information added to the report? I suggest to simply add another row after the pangolin version

Direct assignments via lineage-specific constellation files are performed via scorpio version xxx using constellation versions yyyy 

[hoelzer]

I will also da test w/ public omicron raw data now

[RaverJay]

Yeah the logic was flipped for testing, fixed now - please pull the latest commit

Thanks for testing!

[RaverJay]

[RaverJay]

Maybe we should add a warning if the Pangolin / Nextclade version is very old, because I had this is my first test, obviously the PangoLEARN from July is pretty much useless now

[hoelzer]

Great, looks good now also here! And such a warning would be great if you can easily add it. Bc/ yeah, if someone fails to run the --update command the lineage assingments can be really odd

[RaverJay]

How about this:

And keep the PangoLEARN version also in this top part. Could do the same for NextClade?

[hoelzer]

@RaverJay ! great, having this in the report is even better than in terminal. Yeah, would be also nice for Nextclade then if you can easily add that

[hoelzer]

So looks good I'd say, also just did another regular run again with the current PR version:

[RaverJay]

Nextclade data version is in

[hoelzer]

@RaverJay can this be merged from your side? I also just run a test, looks all good!

[RaverJay]

Well it works for me, but I never trust changes until Chris has run some cloud tests :D

[hoelzer]

;) I agreed w/ him that we merge smaller changes and do prerelases, he will then later also test and then we do a major release