Setting maximum sequence date

Help and Getting Started
1

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

2

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

3

Thanks Richard!

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

4

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
5

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