Update phylogenetic workflow to be consistent with standard data files

The original dengue files were uploaded as:

files/workflows/dengue/sequences_<type>.fasta.zst
files/workflows/dengue/metadata_<type>.tsv.zst

But it may be more inline with the standard data files to update this to

files/workflows/dengue/<type>/sequences.fasta.zst
files/workflows/dengue/<type>/metadata.tsv.zst

This is consistent with the Nextstrain documentation on data files:

https://docs.nextstrain.org/en/latest/reference/data-files.html

phylogenetic/config/config_dengue.yaml

@@ -1,8 +1,8 @@
 # Sequences must be FASTA and metadata must be TSV
 # Both files must be zstd compressed
 # Both files must have a {serotype} expandable field to be replaced by all, denv1-denv4
-sequences_url: "https://data.nextstrain.org/files/workflows/dengue/sequences_{serotype}.fasta.zst"
-metadata_url: "https://data.nextstrain.org/files/workflows/dengue/metadata_{serotype}.tsv.zst"
+sequences_url: "https://data.nextstrain.org/files/workflows/dengue/{serotype}/sequences.fasta.zst"
+metadata_url: "https://data.nextstrain.org/files/workflows/dengue/{serotype}/metadata.tsv.zst"
 
 strain_id_field: "genbank_accession"
 display_strain_field: "strain"

phylogenetic/config/description.md

@@ -2,13 +2,13 @@ We gratefully acknowledge the authors, originating and submitting laboratories o
 
 We curate sequence data and metadata from NCBI as starting point for our analyses. Curated sequences and metadata are available as flat files at:
 
-* [data.nextstrain.org/files/workflows/dengue/sequences_all.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/sequences_all.fasta.zst)
-* [data.nextstrain.org/files/workflows/dengue/metadata_all.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/metadata_all.tsv.zst)
-* [data.nextstrain.org/files/workflows/dengue/sequences_denv1.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/sequences_denv1.fasta.zst)
-* [data.nextstrain.org/files/workflows/dengue/metadata_denv1.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/metadata_denv1.tsv.zst)
-* [data.nextstrain.org/files/workflows/dengue/sequences_denv2.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/sequences_denv2.fasta.zst)
-* [data.nextstrain.org/files/workflows/dengue/metadata_denv2.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/metadata_denv2.tsv.zst)
-* [data.nextstrain.org/files/workflows/dengue/sequences_denv3.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/sequences_denv3.fasta.zst)
-* [data.nextstrain.org/files/workflows/dengue/metadata_denv3.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/metadata_denv3.tsv.zst)
-* [data.nextstrain.org/files/workflows/dengue/sequences_denv4.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/sequences_denv4.fasta.zst)
-* [data.nextstrain.org/files/workflows/dengue/metadata_denv4.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/metadata_denv4.tsv.zst)
+* [data.nextstrain.org/files/workflows/dengue/all/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/all/sequences.fasta.zst)
+* [data.nextstrain.org/files/workflows/dengue/all/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/all/metadata.tsv.zst)
+* [data.nextstrain.org/files/workflows/dengue/denv1/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/denv1/sequences.fasta.zst)
+* [data.nextstrain.org/files/workflows/dengue/denv1/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/denv1/metadata.tsv.zst)
+* [data.nextstrain.org/files/workflows/dengue/denv2/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/denv2/sequences.fasta.zst)
+* [data.nextstrain.org/files/workflows/dengue/denv2/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/denv2/metadata.tsv.zst)
+* [data.nextstrain.org/files/workflows/dengue/denv3/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/denv3/sequences.fasta.zst)
+* [data.nextstrain.org/files/workflows/dengue/denv3/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/denv3/metadata.tsv.zst)
+* [data.nextstrain.org/files/workflows/dengue/denv4/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/denv4/sequences.fasta.zst)
+* [data.nextstrain.org/files/workflows/dengue/denv4/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/denv4/metadata.tsv.zst)