Setting maximum sequence date

Hello,

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,
Jake

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).

best
richard

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.
subsampling:
  custom-county:
    # Focal samples for location
    focal:
      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!