Document new config parameters
Adds three new config parameters to the configuration reference.
@@ -507,6 +507,31 @@ Valid attributes for list entries in `inputs` are provided below.
* type: object
* description: Parameters to configure how to sanitize metadata to a Nextstrain-compatible format.
+### metadata_id_columns
+* type: object
+* description: A list of valid strain name columns in the metadata. The sanitize metadata script will check attempt to use the first of these columns that exists in the metadata. It will exit with an error, if none of the columns exist.
+* default:
+```yaml
+ - "Virus name"
+ - strain
+ - name
+```
+
+### database_id_columns
+* type: object
+* description: A list of columns representing external database ids for metadata records. These unique ids represent a snapshot of data at a specific time for a given strain name. The sanitize metadata script resolves duplicate metadata records for the same strain name by selecting the record with the latest database id. Multiple database id columns allow the script to resolve duplicates when one or more columns has ambiguous values (e.g., "?").
+* default:
+```yaml
+ - "Accession ID"
+ - gisaid_epi_isl
+ - genbank_accession
+```
+
+### error_on_duplicate_strains
+* type: boolean
+* description: Exit the sanitize metadata script with an error when any strains have multiple records in the metadata. The script writes list of all duplicate strains to a file named like `<input>.duplicates.txt` that users can review and use to address unexpected duplicates.
+* default: `false`
+
### parse_location_field
* type: string
* description: Field in the metadata that stores GISAID-formatted location details (e.g., `North America / USA / Washington`) to be parsed into `region`, `country`, `division`, and `location` fields.
