phylogenetic: Use latest ingest data

I missed this in review of #38. The phylogenetic workflow was still pulling from old S3 URLs and not the ingest workflow output data. This commit corrects the S3 URL to the ingest output files and updates the `strain_id_field` config param to use the appropriate ID column from the ingest output.
nextstrain · Apr 11, 2024 · 4226f0c · 4226f0c
1 parent 416c22d
commit 4226f0c
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diff --git a/phylogenetic/config/config_dengue.yaml b/phylogenetic/config/config_dengue.yaml
@@ -1,4 +1,4 @@
-strain_id_field: "accession"
+strain_id_field: "genbank_accession"
 display_strain_field: "strain"
 
 filter:

diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
@@ -21,8 +21,8 @@ rule download:
         metadata = "data/metadata_{serotype}.tsv.zst"
 
     params:
-        sequences_url = "https://data.nextstrain.org/files/dengue/sequences_{serotype}.fasta.zst",
-        metadata_url = "https://data.nextstrain.org/files/dengue/metadata_{serotype}.tsv.zst"
+        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"
     shell:
         """
         curl -fsSL --compressed {params.sequences_url:q} --output {output.sequences}