added skip-scorpio parameter fixes #234

[MarieLataretu]

• for now the default is that scorpio is not skipped and can be skipped with pangolin_skip_scorpio

[replikation]

what is the rationale behind it?

[hoelzer]

what is the rationale behind it?

This is a pangolin issue currently discussed in the community. The problem is that scorpio overwrites correct PangoLearn/Usher assignments. For example this happens for recombinants bc/ there are yet no (?) scorpio constellation files for recombinants. But this also happens for BA.4/5 which is even worse. E.g. see discussions here:

cov-lineages/scorpio#47
cov-lineages/pango-designation#713
cov-lineages/pango-designation#645
cov-lineages/scorpio#46
...

We performed some in-house tests annotation the full DESH collection w/ and w/o scorpio and the results w/o scorpio look more stable and accurate. That's why we want to add a parameter to deactivate scorpio and thus the overwrite of previous pangoLearn/User assignments.

There is also a not yet merged PR (cov-lineages/pangolin#461) about that topic. So maybe the way scorpio works will be changed anyway in the (near) future. But for now, it would be good to have an option to deactivate it.

[hoelzer]

@MarieLataretu but would it be not better to have a general --additional_pango_params ? In case also other options should be given to pangolin in the future...

EDIT: although checking the way you implemented it now is also nice. It's more explicit to have a parameter for deactivation directly in the help

[MarieLataretu]

@MarieLataretu but would it be not better to have a general --additional_pango_params ? In case also other options should be given to pangolin in the future...

EDIT: although checking the way you implemented it now is also nice. It's more explicit to have a parameter for deactivation directly in the help

Yes, it's more explicit and if --additional_pango_params is per default --skip-scorpio it's kind of hard to turn it off on the command line.

Of course --additional_pango_params would be more flexible.

[replikation]

but it sounds like it would be better to deactivate it by default or did i misunderstand this?

[MarieLataretu]

I wasn't sure about changing the default behavior - I can change that to skip scorpio per default, if you agree

[hoelzer]

Yeah, that's the question. We could also deactivate it by default and write that in the release notes (citing also the discussions I mentioned here)? Could be just that when the Pango devs change also the default behavior in the tool itself we also might have to change that back.

Assuming that many people just use the pipeline and report the results it might be even good we make this decision based on the current discussions and tests. So from my site also +1 to make this the current default

[replikation]

i mean most users are probably not reading this so i would just set the defaults to the best practice. :)

[MarieLataretu]

I changed the default to true.
Skipping scorpio can be deactivated with --pangolin_skip_scorpio false

[replikation]

can we changed it to just --scorpio to activate it? its more understandable for the user

[hoelzer]

@replikation yeah, I like that it's not so DoppeltGemoppelt

btw the current release vs/ Maries master branch w/ scorpio deactivated:
https://twitter.com/martinhoelzer/status/1537769594546442241

[MarieLataretu]

Done.
Per default is --scorpio false, so --skip-scorpio is added to pangolin.

[replikation]

Perfect. I'll run some tests and then merge. Thank you