Move fetch_sequences.smk to fetch_from_ncbi.smk

This is a more accurate name for the rule, since it fetches from NCBI and
matches the pathogen-repo-template/ingest/ncbi_fetch_sequences.smk rule.

ingest/Snakefile

@@ -54,7 +54,7 @@ rule all:
         _get_all_targets,
 
 
-include: "rules/fetch_sequences.smk"
+include: "rules/fetch_from_ncbi.smk"
 include: "rules/transform.smk"
 
 

ingest/rules/fetch_sequences.smk → ingest/rules/fetch_from_ncbi.smk

@@ -7,6 +7,10 @@ defined in the config. If adding other sources, add a new rule upstream
 of rule `fetch_all_sequences` to create the file `data/{source}.ndjson` or the
 file must exist as a static file in the repo.
 
+Fetch with NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/)
+    - requires `ncbi_taxon_id` config
+    - Only returns metadata fields that are available through NCBI Datasets
+
 Produces final output as
 
     sequences_ndjson = "data/sequences.ndjson"