Adds an argument to the script for flagging outliers that accepts a file with a list of strains to keep in the output tree even if they are outliers and updates the core workflow logic to use this argument whenever builds define a list of strains to force-include. This change fixes a bug when older titer reference strains (e.g., A/Wisconsin/588/2019 for H1N1pdm) get flagged as outliers in the tree and dropping them causes downstream titer analyses to fail. Our choice to force-include these strains in the build should override the automated outlier detection.
Testing
[x] Tested manually with H1 build where a reference strain was being excluded
Description of proposed changes
Adds an argument to the script for flagging outliers that accepts a file with a list of strains to keep in the output tree even if they are outliers and updates the core workflow logic to use this argument whenever builds define a list of strains to force-include. This change fixes a bug when older titer reference strains (e.g., A/Wisconsin/588/2019 for H1N1pdm) get flagged as outliers in the tree and dropping them causes downstream titer analyses to fail. Our choice to force-include these strains in the build should override the automated outlier detection.
Testing