ncov
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Allow build-specific --narrow-bandwidth param in frequencies
Description of proposed changes
This is a bug fix PR. There was a bug in the current behavior where the rule frequencies
was calling config["frequencies"]["narrow_bandwidth"]
. This resulted in --narrow-bandwidth to be fixed to whatever was specified in parameters.yaml
. However, we were relying on build-specific settings to differentiate behavior in the all-time
vs 6m
vs 2m
vs 1m
builds, ala:
frequencies
global_1m:
narrow_bandwidth: 0.019
This PR fixes this issue and allows overriding of narrow_bandwidth
in parameters.yaml
by build-specific settings. It also provides a genuine default (equal to augur default) so that parameters.yaml
doesn't have to always specify narrow_bandwidth
.
Additionally, this PR removes the build-specific setting for recent_days_to_censor
. This setting wasn't actually being applied in a build-specific fashion and so we had been always using the workflow default of 0
. I decided to stick with this.
Testing
I've tested locally and via trial build. Trail builds are visible at: