Nextclade: QC tuning for SH dataset #40
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The Mumps Nextclade dataset had been reporting both a "Clade" and a "MuV_genotype" column. This change only reports the "Clade" assignment as the second is redundant for the user. This change also allows us to drop the hard coded nextclade_extension specification in the auspice_config files since pathogen.json already has this information and having both would risk settings getting out of sync and confusion during debugging.
Add documentation on where clade_membership is being spiked in or inferred from a fall back column. Clearly use clade_membership during the genome filtering step, even though MuV_genotype should have equivalent behavior.
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Description of proposed changes
Since the genome Nextclade dataset has QC, initialized QC parameters for sh Nextclade dataset. However, I could use some help on picking thresholds...
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