Use augur subsample

[victorlin]

This workflow's subsampling is implemented by a single augur filter call. It works fine, but is limited in capabilities and not portable across pathogen repos.

Description of work

1. Update the configuration from:

   mumps/phylogenetic/defaults/config.yaml

   Lines 13 to 20 in 53c0a6e

   	filter:
   	min_length: 8000
   	group_by: country year month MuV_genotype division
   	exclude: "{build}/exclude.txt"
   	include: "{build}/include.txt"
   	specific:
   	north-america: --subsample-max-sequences 4000 --min-date 2006 --query "region=='North America' & (MuV_genotype=='G')"
   	global: --subsample-max-sequences 4000 --min-date 1950

   to something more generic and customizable.

2. Replace the filter rule with a rule that calls augur subsample.

   This rule should:

   1. Allow concurrent sample runs with threads
   2. Pass a dump of Snakemake's config as a YAML file to --config
   3. Extract the relevant configuration using --config-section
   4. Allow Snakemake to intelligently handle conditional runs of the subsample rule in the case of config changes.
   5. Be compatible with external analysis directories (nextstrain run)