Setting maximum sequence date


Is there an way to set the maximum sequence date when using the snakemake script? For example, if I only wanted to select samples collected before 2020-04-01.

Thanks for your help,

Yes, you can do this! augur filter has a flag --max-date:

you should be able to use this as

augur filter --max-date 2020-04-01

(and the other arguments for sequences, metadata, and output of course).


Thanks Richard!

Is there an option to set this paramter in the builds.yaml file when running the snakemake workflow?

Not currently (you’d have to modify the actual snakemake file) but you can achieve the same result by adding the "max_date" field to each of your subsampling schemes in your build config. E.g. using my_profiles/example/builds.yaml

# Define custom subsampling logic for county-level builds.
    # Focal samples for location
      group_by: "year month"
      max_date: "2020-04-01" # <-- add this to each scheme
      seq_per_group: 300

Ah! That should work for me, thanks for your help!