fixup: forgot the example files connection

nextstrain · May 8, 2024 · 30b1d5a · 30b1d5a
1 parent dd45b63
commit 30b1d5a
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
@@ -35,7 +35,7 @@ rule decompress:
         sequences = "data/sequences_{serotype}.fasta.zst",
         metadata = "data/metadata_{serotype}.tsv.zst"
     output:
-        sequences = "data/genome/sequences_{serotype}.fasta",
+        sequences = "data/sequences_{serotype}.fasta",
         metadata = "data/metadata_{serotype}.tsv"
     shell:
         """
@@ -52,7 +52,7 @@ rule filter:
       - excluding strains with missing region, country or date metadata
     """
     input:
-        sequences = "data/{gene}/sequences_{serotype}.fasta",
+        sequences = "data/sequences_{serotype}.fasta",
         metadata = "data/metadata_{serotype}.tsv",
         exclude = config["filter"]["exclude"],
     output:

diff --git a/phylogenetic/rules/prepare_sequences_E.smk b/phylogenetic/rules/prepare_sequences_E.smk
@@ -41,7 +41,7 @@ rule align_and_extract_E:
     Cutting sequences to the length of the E gene reference sequence
     """
     input:
-        sequences = "data/genome/sequences_{serotype}.fasta",
+        sequences = "data/sequences_{serotype}.fasta",
         reference = "results/config/reference_{serotype}_E.fasta"
     output:
         sequences = "results/E/sequences_{serotype}.fasta"