Move hardcode filter query into configuration files

[huddlej]

Description

The following hardcoded filter parameter appears at the start of the phylogenetic workflow:

mpox/phylogenetic/rules/prepare_sequences.smk

Line 85 in 2ce0d92

--query "(QC_rare_mutations == 'good' | QC_rare_mutations == 'mediocre')" \

When the user's metadata does not have the two columns referenced in that query (as happens when analyzing data from GISAID, for example), augur filter produces the following output:

WARNING: Column 'QC_rare_mutations' does not exist in the metadata file. Ignoring it.
ERROR: Query contains a column that does not exist in metadata.

Although that output comes across as an augur bug (that a warning is also an error), the proximal issue is that the workflow hardcodes parameters that the user cannot override without changing the workflow itself.

Proposed solution

I suggest moving the query string into the config files for the various workflows, specifically moving the hardcoded query into the top-level filter section of each config file (e.g., defaults/mpxv/config.yaml). Then users who want to analyze data without the fields referenced in that query can create their own config file.

[corneliusroemer]

Even simpler: check for presence of that column and make the filter dependent on whether it's present or not.

I'd prefer automatic stuff over configure.

Also, people should in general just fork things and make the changes they want themselves.