Update AA mutation calling module

BCCDC-PHL / fluviewer-nf

Nextflow pipeline for influenza A whole genome sequence analysis

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Update AA mutation calling module #41

Open jpalmer37 opened 6 days ago

jpalmer37 commented 6 days ago

The AA mutation calling module is in need of an upgrade to improve its formatting, simplicity, and start-position logic. The following changes will be implemented:

integrating the BLASTX search into the Python script itself, to remove a required argument
changing the script logic to utilize BLASTX start positions for reliability
fixing title headers in the output TSV
updating the BLASTX database as the start positions of certain segments (HA) are incorrect

jpalmer37 commented 6 days ago

This was deemed not necessary. Original logic was already quite robust.

~~changing the script logic to utilize BLASTX start positions for reliability~~