Move the ncbi field map to config

To be consistent with the nextclade-field-map.tsv, move the ncbi-field-map.tsv to config.
nextstrain · Oct 31, 2023 · 66a45df · 66a45df
1 parent 9ff822f
commit 66a45df
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diff --git a/ingest/config/config.yaml b/ingest/config/config.yaml
@@ -2,6 +2,8 @@
 sources: ['genbank']
 # Pathogen NCBI Taxonomy ID
 ncbi_taxon_id: '10244'
+# Renames the NCBI dataset headers
+ncbi_field_map: 'source-data/ncbi-dataset-field-map.tsv'
 
 # Params for the transform rule
 transform:

diff --git a/ingest/workflow/snakemake_rules/fetch_sequences.smk b/ingest/workflow/snakemake_rules/fetch_sequences.smk
@@ -80,7 +80,7 @@ rule format_ncbi_dataset_report:
     # The only fields we do not have equivalents for are "title" and "publications"
     input:
         dataset_package="data/ncbi_dataset.zip",
-        ncbi_field_map="source-data/ncbi-dataset-field-map.tsv",
+        ncbi_field_map=config["ncbi_field_map"],
     output:
         ncbi_dataset_tsv=temp("data/ncbi_dataset_report.tsv"),
     params: