add exclude parameter to filter_subsample_sequences task and augur_from_msa workflow; improve handling of whitespace, empty lines, or absent last-line trailing newline in input include/exclude files

[tomkinsc]

• add an exclude_list parameter to the filter_subsample_sequences task for use in the augur_from_msa workflow
  • (exclusions are processed after considering IDs designated explicitly as those to keep)
• add optional inputs to filter_subsample_sequences so include/exclude IDs can be specified in string inputs as space-delimited lists
  • (such IDs are combined with any coming from corresponding include/exclude files)
• improve handling of whitespace, empty lines, or absent last-line trailing newline in input include/exclude files

This does not alter the prior behavior that input sequences are passed through to the output unaltered if no filtering is specified.