[TheiaCoV] Reorder flu assembly segments in largest-to-smallest order

[emily-smith1]

🆒

📌 Explain the Request

Re-ordering of the flu segments in the assembly_fasta file output by TheiaCoV in largest to smallest order: PB1, PB2, PA, HA, NP, NA, MP, NS, in accordance with Nextstrain/UShER formatting.

[Michal-Babins]

Is the expectation here to sort the segments and overwrite the file in place of the assembly fasta OR to save the ordered output to a modified file (ordered_assembly.fasta)?

[emily-smith1]

I'd suggest overwriting the existing assembly_fasta file to cut down on the number of output columns, unless the existing order is necessary for something downstream.

[Michal-Babins]

Did some testing against my branch and was able to confirm the assembly fasta correctly represents the ordered segments (PB2,PB1,PA,HA,NP,NA,MP,NS) after running end to end.

Job history relating to this run can be found here, showing 10 successful runs.

You can check all the assemblies in the flu_testing data table to confirm the assemblies look as expected.