This was not an issue when we were re-processing all data de novo, but now that we are storing sequences and metadata in a local database, there is a risk that a sample of lineage X becomes re-labelled lineage Y. As a result, we would have duplicate records in the database. This would cause the pipeline to crash when it attempts to insert a new record with accession number as unique key, which collides with the existing record with the same key. This would be easy to fix by modifying the database insert statement.
This was not an issue when we were re-processing all data de novo, but now that we are storing sequences and metadata in a local database, there is a risk that a sample of lineage X becomes re-labelled lineage Y. As a result, we would have duplicate records in the database. This would cause the pipeline to crash when it attempts to insert a new record with accession number as unique key, which collides with the existing record with the same key. This would be easy to fix by modifying the database insert statement.