Add configurable staged input files for the `phylogenetic` github action

[j23414]

Description of proposed changes

Fixes https://github.com/nextstrain/dengue/issues/49

Related issue(s)

• https://github.com/nextstrain/dengue/issues/49
• Nice to have to test a future PR for https://github.com/nextstrain/dengue/compare/main...consistent-serotype-genotype-column-names
• which is addressing Issue: https://github.com/nextstrain/dengue/issues/41

Checklist

• [x] Checks pass
• [x] GH test at https://github.com/nextstrain/dengue/actions/runs/9149432810

Serotype expanded as expected

rule download:
    output: data/sequences_denv3.fasta.zst, data/metadata_denv3.tsv.zst
    jobid: 86
    reason: Missing output files: data/sequences_denv3.fasta.zst, data/metadata_denv3.tsv.zst
    wildcards: serotype=denv3
    resources: tmpdir=/tmp
        curl -fsSL --compressed https://data.nextstrain.org/files/workflows/dengue/trials/serogeno20240518/sequences_denv3.fasta.zst --output data/sequences_denv3.fasta.zst
        curl -fsSL --compressed https://data.nextstrain.org/files/workflows/dengue/trials/serogeno20240518/metadata_denv3.tsv.zst --output data/metadata_denv3.tsv.zst