Prepare phylogenetic workflow for Nextclade workflow

[j23414]

Description of proposed changes

Following the plan laid out in #21 (comment)

This PR is making some minor updates to the phylogenetic workflow to prepare for the Nextclade workflow.

Related issue(s)

• Set root reference in phylogenetic builds #56
• Add workflow for producing the Nextclade dengue dataset #21
• Add workflow for producing the Nextclade dengue dataset #25

Checklist

• Checks pass
• Check a phylogenetic run (see run here)

	genome	E gene
all	all/genome	all/E
denv1	denv1/genome	denv1/E
denv2	denv2/genome	denv2/E
denv3	denv3/genome	denv3/E
denv4	denv4/genome	denv4/E

[genehack]

1. is it worth putting this closer to the --exclude option to make it clear both are in play?
2. is it worth a comment explaining how --exclude and --include interact, or is that assumed to be table-stakes knowledge for anybody that might want to modify this?

[j23414]

1. I meant to put --include next to --exclude. I got faked out by --exclude-where, thanks for flagging!
2. The comments explaining how --exclude and --include interact is mostly pointing to augur filter docs, aka, not commented here. However, when I get into lineage defining strains, the "include.txt" may need to be split out into DENV1-DENV4 and I haven't figured out the design for that yet.

Potential design 1: Keep separate include_{serotype}.txt files

Potential design 2: Create a snakemake rule that takes a lineage.tsv and creates include_{serotype}.txt and append_clade_membership_{serotype}.tsv... I haven't written this up yet.

[j23414]

assumed to be table-stakes knowledge for anybody that might want to modify this [include.txt]

Actually this is a good point, I went with Potential design 1 as easier to explain to other people. 3ed18d2

Fixup of include next to exclude in c6e589f