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Change relative internal anchor links to full URIs [#1133]
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genehack committed Aug 13, 2024
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## New features since last version update

- 11 August 2021: Add support for "Sequences" and "Patient status metadata" downloads from GISAID's search interface including [documentation in the tutorial of how to use these data](../guides/data-prep.html#curate-data-from-gisaid-search-and-downloads). ([#701](https://github.com/nextstrain/ncov/pull/701))
- 11 August 2021: Add support for "Sequences" and "Patient status metadata" downloads from GISAID's search interface including [documentation in the tutorial of how to use these data](https://docs.nextstrain.org/projects/ncov/en/latest/guides/data-prep/gisaid-search.html). ([#701](https://github.com/nextstrain/ncov/pull/701))
- 6 August 2021: We've replaced the mechanisms that support remote file inputs (e.g. `s3://` URLs) to improve internal workflow structure, extend support to `gs://`, `http://`, and `https://` URLs, and expand support for compressed inputs.
Our [remote file inputs documentation](remote_inputs) is updated to reflect the changes.

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## v7 (27 May 2021)

For more details about this release, see [the configuration reference for the new "sanitize metadata" parameters](configuration.html#sanitize_metadata) and [the corresponding pull request](https://github.com/nextstrain/ncov/pull/640).
For more details about this release, see [the configuration reference for the new "sanitize metadata" parameters](https://docs.nextstrain.org/projects/ncov/en/latest/reference/workflow-config-file.html#sanitize-metadata) and [the corresponding pull request](https://github.com/nextstrain/ncov/pull/640).

### Major changes

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## New features since last version update

- 25 May 2021: Support custom Auspice JSON prefixes with a new configuration parameter, `auspice_json_prefix`. [See the configuration reference for more details](configuration.html#auspice_json_prefix). ([#643](https://github.com/nextstrain/ncov/pull/643))
- 25 May 2021: Support custom Auspice JSON prefixes with a new configuration parameter, `auspice_json_prefix`. [See the configuration reference for more details](https://docs.nextstrain.org/projects/ncov/en/latest/reference/workflow-config-file.html#auspice-json-prefix). ([#643](https://github.com/nextstrain/ncov/pull/643))

## v6 (20 May 2021)

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### Major changes

- Drop support for old sequence/metadata inputs. This change removes support for the `config["sequences"]` and `config["metadata"]` starting points for the workflow in favor of the more flexible [`config["inputs"]` format](configuration.html#inputs).
- Drop support for old sequence/metadata inputs. This change removes support for the `config["sequences"]` and `config["metadata"]` starting points for the workflow in favor of the more flexible [`config["inputs"]` format](https://docs.nextstrain.org/projects/ncov/en/latest/reference/workflow-config-file.html#inputs).
- Use `nextalign` for alignment instead of `mafft`. This change completely removes support for `mafft` in favor of `nextalign`. Future versions may reinstate `mafft` support as part of `augur align` updates.

### Minor changes
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