phylogenetic: Use augur subsample

[victorlin]

Description of proposed changes

The augur subsample command is built to replace the pattern of multiple intermediate augur filter calls with simpler Snakemake rules and configuration.

Note that this is a breaking change and the old configuration will no longer work.

Due to limitations of augur subsample, I had to move the "include" file from the top level of config to under a sample. For configs with multiple samples, I chose the sample somewhat arbitrarily. We could easily update augur subsample to accept the --include CLI option, but I'm not sure it's necessary given this easy workaround.

Related issue(s)

nextstrain/augur#635

Checklist

• Tested locally with snakemake --cores 1 --configfile build-configs/ci/config.yaml

  output

  Validating schema of 'results/hmpxv1/run_config.yaml'...
  [non_b1] 22 strains were dropped during filtering
  [non_b1]        1 was dropped because of 'lineage=B.1'
  [non_b1]        1 was dropped because of 'lineage=B.1.1'
  [non_b1]        1 was dropped because of 'lineage=B.1.2'
  [non_b1]        1 was dropped because of 'lineage=B.1.3'
  [non_b1]        1 was dropped because of 'lineage=C.1'
  [non_b1]        1 was dropped because of 'lineage=B.1.4'
  [non_b1]        1 was dropped because of 'lineage=B.1.5'
  [non_b1]        1 was dropped because of 'lineage=B.1.6'
  [non_b1]        1 was dropped because of 'lineage=B.1.7'
  [non_b1]        1 was dropped because of 'lineage=B.1.8'
  [non_b1]        1 was dropped because of 'lineage=B.1.9'
  [non_b1]        1 was dropped because of 'lineage=B.1.10'
  [non_b1]        1 was dropped because of 'lineage=B.1.11'
  [non_b1]        1 was dropped because of 'lineage=B.1.12'
  [non_b1]        1 was dropped because of 'lineage=B.1.13'
  [non_b1]        1 was dropped because of 'lineage=B.1.14'
  [non_b1]        1 was dropped because of 'lineage=B.1.15'
  [non_b1]        1 was dropped because of 'lineage=B.1.16'
  [non_b1]        1 was dropped because of 'lineage=B.1.17'
  [non_b1]        1 was dropped because of 'lineage=B.1.18'
  [non_b1]        1 was dropped because of 'lineage=B.1.19'
  [non_b1]        1 was dropped because of 'lineage=B.1.20'
  [non_b1]        0 were dropped because of subsampling criteria
  [non_b1] 9 strains passed all filters
  [b1] Sampling at 300 per group.
  [b1] 0 strains were dropped during filtering
  [b1]    0 were dropped because of subsampling criteria
  [b1] 31 strains passed all filters
  0 strains were dropped during filtering
          31 were dropped by `--exclude-all`
          9 were added back because they were in /var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/sample_non_b1__kzu7ygo
          31 were added back because they were in /var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/sample_b1_ilqjjac2
  31 strains passed all filters
  

• Release augur subsample
• Checks pass
• Update changelog