Document new features in change log and configuration reference

nextstrain · May 26, 2021 · e45903e · e45903e
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diff --git a/docs/change_log.md b/docs/change_log.md
@@ -5,6 +5,7 @@ We also use this change log to document new features that maintain backward comp
 
 ## New features since last version update
 
+ - 26 May 2021: Support default (full) GISAID metadata and sequences from the "Download packages" interface by converting this default format into Nextstrain-compatible metadata. Additionally, the workflow now deduplicates metadata and sequences at the beginning and also supports reading metadata and sequences directly from GISAID's tar archives. ([#640](https://github.com/nextstrain/ncov/pull/640))
  - 25 May 2021: Support custom Auspice JSON prefixes with a new configuration parameter, `auspice_json_prefix`. [See the configuration reference for more details](https://nextstrain.github.io/ncov/configuration.html#auspice_json_prefix). ([#643](https://github.com/nextstrain/ncov/pull/643))
 
 ## v6 (20 May 2021)

diff --git a/docs/configuration.md b/docs/configuration.md
@@ -497,6 +497,25 @@ Valid attributes for list entries in `inputs` are provided below.
 * description: A list of prefixes to strip from strain names in metadata and sequence records to maintain consistent strain names when analyzing data from multiple sources.
 * default: `["hCoV-19/", "SARS-CoV-2/"]`
 
+## sanitize_metadata
+* type: object
+* description: Parameters to configure how to sanitize metadata to a Nextstrain-compatible format.
+
+### 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.
+* default: `Location`
+
+### rename_fields
+* type: array
+* description: List of key/value pairs mapping fields in the input metadata to rename to another value in the sanitized metadata.
+* default: `["Virus name=strain", "Collection date=date"]`
+
+### standardize_columns
+* type: boolean
+* description: Standardize column names by lowercasing and replacing all whitespace with underscores. This operation happens after renaming fields.
+* default: `true`
+
 ## subsampling
 * type: object
 * description: Schemes for subsampling data prior to phylogenetic inference to avoid sampling bias or focus an analysis on specific spatial and/or temporal scales. [See the SARS-CoV-2 tutorial for more details on defining subsampling schemes](https://docs.nextstrain.org/en/latest/tutorials/SARS-CoV-2/steps/customizing-analysis.html#subsampling).