Pull data from "SARS-CoV-2 Sequence Data from Germany"

[joverlee521]

Context

Similar to #329, there has been a significant drop off in sequences from Germany in the NCBI data since ~April 2022 (this issue was originally raised by @corneliusroemer in Slack):

Description

We can update the open pipeline to pull metadata and sequences directly from the "SARS-CoV-2 Sequence Data from Germany" GitHub repo.

Possible solution

Similar solutions from #329 will apply here.

[joverlee521]

I think the solution for directly pulling RKI sequences will be similar to my ideas for the COG-UK data.

The different step here might be how to remove the RKI sequences from the GenBank data. I have not found an accession linkage file for the RKI data. However, we can do a blanket removal of all sequences linked to the RKI BioProject.

[corneliusroemer]

We could simply remove all German sequences uploaded to Genbank from March 2022 onwards and only spike from Germany's repo from that date onwards as a quick fix.
This would be 80/20, more effort may not be worth it.

[joverlee521]

Resolved by #365