Covid19Data Portal missing Lineages handling

[johausmann]

I noticed another problem after the Covid19DataPortal update. We get the lineage information from the portal directly and store it in the database. After the Data Portal update I looked at the lineages plot and saw that it does not go further than October last year. I then checked the samples from the update and saw that of the 462.957 new assemblies, 348.256 have no lineage in the repository. Of the remaining assemblies, the newest ones have a collection_date < 2022-02-28, so the plot shows no 2023 lineages.

[johausmann]

Okay, we need to address the following items.

• Update Covid19DataPortal accessor to be aware of missing lineage.
• Update Processor and Pipeline module to optionally call Pangolin in case of missing lineage.
  • Pipeline call without '--skip_pangolin'
  • Add mode to check if mutations are present in database and VCF file exists --> run Pangolin only.
• Update Covigator NGS pipeline to have a mode for Pangolin only.
• Enable loading of Pangolin results from assemblies into database (code is present, needs to called based on call).