subsample: Improve --output-log

[victorlin]

from #1879 (comment)

Currently, --output-log is passed directly to the final augur filter call. This exposes implementation details and can be made better.

Possible solutions

Use --output-log in all the intermediate samples and merge them together.

[victorlin]

Passing --output-log directly to the final augur filter call produces a somewhat meaningful file. Example from a test in the PR that adds this functionality:

  strain	filter	kwargs
  BRA/2016/FC_6706	filter_by_exclude_all	[]
  HND/2016/HU_ME59	filter_by_exclude_all	[]
  COL/FLR_00024/2015	filter_by_exclude_all	[]
  EcEs062_16	filter_by_exclude_all	[]
  COL/FLR_00008/2015	filter_by_exclude_all	[]
  SG_018	filter_by_exclude_all	[]
  Colombia/2016/ZC204Se	filter_by_exclude_all	[]
  ZKC2/2016	filter_by_exclude_all	[]
  DOM/2016/BB_0059	filter_by_exclude_all	[]
  PRVABC59	filter_by_exclude_all	[]
  DOM/2016/BB_0183	filter_by_exclude_all	[]
  VEN/UF_1/2016	filter_by_exclude_all	[]
  DOM/2016/BB_0059	force_include_strains	"[[""include_file"", ""/var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/cramtests-rql0p54a/tmp/sample_A_fn68ae17""]]"
  SG_018	force_include_strains	"[[""include_file"", ""/var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/cramtests-rql0p54a/tmp/sample_A_fn68ae17""]]"
  DOM/2016/BB_0183	force_include_strains	"[[""include_file"", ""/var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/cramtests-rql0p54a/tmp/sample_A_fn68ae17""]]"
  VEN/UF_1/2016	force_include_strains	"[[""include_file"", ""/var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/cramtests-rql0p54a/tmp/sample_A_fn68ae17""]]"
  HND/2016/HU_ME59	force_include_strains	"[[""include_file"", ""/var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/cramtests-rql0p54a/tmp/sample_B_5cl5cxc9""]]"
  SG_018	force_include_strains	"[[""include_file"", ""/var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/cramtests-rql0p54a/tmp/sample_B_5cl5cxc9""]]"
  DOM/2016/BB_0059	force_include_strains	"[[""include_file"", ""/var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/cramtests-rql0p54a/tmp/sample_B_5cl5cxc9""]]"
  DOM/2016/BB_0183	force_include_strains	"[[""include_file"", ""/var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/cramtests-rql0p54a/tmp/sample_B_5cl5cxc9""]]"
  VEN/UF_1/2016	force_include_strains	"[[""include_file"", ""/var/folders/t6/1bw47jm52szgxdfnlbgvchgc0000gn/T/cramtests-rql0p54a/tmp/sample_B_5cl5cxc9""]]"

I don't think this is great, and don't plan to close the issue if/when it gets merged. A proper --output-log file shouldn't expose implementation details, but this is better than nothing given that a potential early user upvoted the initial idea of having --output-log for debugging.