A user requested that for Flu nextclade outputs for AA subs and dels, instead of outputting NA when nothing is found, write None.
"NA" is easily confused with the abbreviation for Neuraminidase.
Example:
:books: Context
FYI this will likely impact all other organisms that nextclade is run on, so it would be a somewhat broad change to the output format. With an impactful change like this, let's consider what the downstream impacts are, try to mitigate them, and warn users about the change in future versions
:cool:
:pushpin: Explain the Request
A user requested that for Flu nextclade outputs for AA subs and dels, instead of outputting
NAwhen nothing is found, writeNone."NA" is easily confused with the abbreviation for Neuraminidase.
Example:
:books: Context
FYI this will likely impact all other organisms that nextclade is run on, so it would be a somewhat broad change to the output format. With an impactful change like this, let's consider what the downstream impacts are, try to mitigate them, and warn users about the change in future versions
I believe this bit of code adds
NAto the output string: https://github.com/theiagen/public_health_bioinformatics/blob/d0377e139855252e15b57d7699aa6f5abb510996/tasks/taxon_id/task_nextclade.wdl#L179:chart_with_upwards_trend: Desired Behavior
Output
Noneinstead ofNA:information_source: Additional Information