Prepare phylogenetic workflow for Nextclade workflow

[j23414]

Description of proposed changes

Following the plan laid out in https://github.com/nextstrain/dengue/issues/21#issuecomment-2128162523

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

Related issue(s)

• https://github.com/nextstrain/dengue/issues/56
• https://github.com/nextstrain/dengue/issues/21
• https://github.com/nextstrain/dengue/pull/25

Checklist

• [x] 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