Resolve filepaths within augur subsample and add them as rule input

[victorlin]

Note

Based on #89, nextstrain/augur#1918

Description of proposed changes

This removes workflow-specific config modifications and takes advantage of a Snakemake feature.

Related issue(s)

• subsample: Improve relative filepath search augur#1897

Checklist

• Details

  Tested `nextstrain run` locally

  $ nextstrain run --augur=/Users/vlin/repos/nextstrain/augur . phylogenetic tmp
  …
  localrule filter:
      input: results/run_config.yaml, data/sequences.fasta, data/metadata.tsv, /nextstrain/pathogen/phylogenetic/defaults/include_strains_genome.txt, /nextstrain/pathogen/phylogenetic/defaults/dropped_strains.txt
  …
  Validating schema of 'results/run_config.yaml'...
  24156 strains were dropped during filtering
          3 were dropped because they were in /nextstrain/pathogen/phylogenetic/defaults/dropped_strains.txt
          4 were dropped because they were earlier than 1950.0 or missing a date
          23510 were dropped because they were shorter than the minimum length of 5000bp when only counting standard nucleotide characters A, C, G, or T (case-insensitive)
          150 were dropped during grouping due to ambiguous year information
          6 were added back because they were in /nextstrain/pathogen/phylogenetic/defaults/include_strains_genome.txt
          495 were dropped because of subsampling criteria
  689 strains passed all filters

• Checks pass

• Update changelog

• Pre-merge: drop e751070

• Pre-merge: update changelog to replace TBD