Use centralized scripts for NCBI Virus

`fetch-from-ncbi-virus` from the subrepo is a copy of `fetch-from-genbank` with some extra options. It can be used as-is since the new options are not required. Remove the copy in this repo and update references. The supporting scripts `csv-to-ndjson` and `genbank-url` can also be removed.
nextstrain · Aug 30, 2023 · 111020e · 111020e
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diff --git a/ingest/README.md b/ingest/README.md
@@ -84,7 +84,7 @@ These are optional environment variables used in our automated pipeline for prov
 ### GenBank data
 
 GenBank sequences and metadata are fetched via NCBI Virus.
-The exact URL used to fetch data is constructed in `bin/genbank-url`.
+The exact URL used to fetch data is constructed by `vendored/ncbi-virus-url`.
 
 ## `ingest/vendored`
 

diff --git a/ingest/bin/csv-to-ndjson b/ingest/bin/csv-to-ndjson
diff --git a/ingest/bin/fetch-from-genbank b/ingest/bin/fetch-from-genbank
diff --git a/ingest/bin/genbank-url b/ingest/bin/genbank-url
diff --git a/ingest/workflow/snakemake_rules/fetch_sequences.smk b/ingest/workflow/snakemake_rules/fetch_sequences.smk
@@ -20,7 +20,7 @@ rule fetch_from_genbank:
     retries: 5  # Requires snakemake 7.7.0 or later
     shell:
         """
-        ./bin/fetch-from-genbank 10244 > {output.genbank_ndjson}
+        ./vendored/fetch-from-ncbi-virus 10244 > {output.genbank_ndjson}
         """
-Original file line number
+Diff line change
@@ Expand Up / @@ -20,7 +20,7 @@ rule fetch_from_genbank: @@
         retries: 5  # Requires snakemake 7.7.0 or later
         shell:
             """
-            ./bin/fetch-from-genbank 10244 > {output.genbank_ndjson}
+            ./vendored/fetch-from-ncbi-virus 10244 > {output.genbank_ndjson}
             """
@@ Expand Down @@