fix: enable staged input files for phylogenetic github action

nextstrain · May 19, 2024 · 0b02617 · 0b02617
1 parent 7fa4e2a
commit 0b02617
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/phylogenetic/config/config_dengue.yaml b/phylogenetic/config/config_dengue.yaml
@@ -1,3 +1,9 @@
+# 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"
+
 strain_id_field: "genbank_accession"
 display_strain_field: "strain"
 

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/workflows/dengue/sequences_{serotype}.fasta.zst",
-        metadata_url = "https://data.nextstrain.org/files/workflows/dengue/metadata_{serotype}.tsv.zst"
+        sequences_url = config["sequences_url"],
+        metadata_url = config["metadata_url"],
     shell:
         """
         curl -fsSL --compressed {params.sequences_url:q} --output {output.sequences}