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| # CHANGELOG | ||
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| We use this CHANGELOG to document breaking changes, new features, bug fixes, | ||
| and config value changes that may affect both the usage of the workflows and | ||
| the outputs of the workflows. | ||
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| ## 2024 | ||
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| * 24 February 2024: Move accession to the first column of `metadata_all.tsv`. ([PR #36](https://github.com/nextstrain/zika/pull/36)) | ||
| * 05 February 2024: Harmonize with [pathogen repo guide](https://github.com/nextstrain/pathogen-repo-guide) ([PR #31](https://github.com/nextstrain/zika/pull/31)) | ||
| * 19 January 2024: Add a Quickstart section to the top level README. ([PR #30](https://github.com/nextstrain/zika/pull/30)) | ||
| * 19 January 2024: Add ingest pipeline and restructure phylogeny pipeline. ([PR #28](https://github.com/nextstrain/zika/pull/28)) | ||
| * The addition of the ingest pipeline is a major change. Instead of relying on the `fauna` database, this introduces retrieving data from NCBI datasets directly and conducting subsequent curation. | ||
| * The restructuring of the `phylogenetic` pipeline into a dedicated directory keeps the two workflows modular, and conforms to the [pathogen repo guide](https://github.com/nextstrain/pathogen-repo-guide). | ||
| * Documenting and providing the USVI data in the `phylogenetic/data` directory. | ||
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| ## 2023 | ||
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| * 04 May 2023: Stylistic changes to make the Snakemake code conform to documented [Nextstrain Snakemake Styleguide](https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html). ([PR #27](https://github.com/nextstrain/zika/pull/27)) | ||
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| ## 2022 | ||
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| * 14 October 2022: Use zstd compression instead of xz and gzip. ([PR #23](https://github.com/nextstrain/zika/pull/23)) | ||
| * 26 August 2022: Remove cores flag as it is no longer needed in nextstrain cli. ([PR #22](https://github.com/nextstrain/zika/pull/22)) | ||
| * 14 April 2022: Specify `--cores all` for `nextstrain build .` to be compatible with snakemake>5.11.0. ([PR #19](https://github.com/nextstrain/zika/pull/19)) | ||
| * 01 April 2022: CI: Use a centralized pathogen repo CI workflow. ([PR #17](https://github.com/nextstrain/zika/pull/17)) | ||
| * 01 April 2022: Migrate CI to GitHub Actions. ([PR #16](https://github.com/nextstrain/zika/pull/16)) | ||
| * 22 March 2022: Use Snakemake HTTP remote to download starting points and switch to uncompressed example data. ([PR #15](https://github.com/nextstrain/zika/pull/15)) | ||
| * 14 March 2022: Use the python 3.7 miniconda installer to fix error in travis test. ([PR #14](https://github.com/nextstrain/zika/pull/14)) | ||
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| ## 2021 | ||
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| * 09 November 2021: CI: Upgrade setuptools suite prior to installation. ([PR #13](https://github.com/nextstrain/zika/pull/13)) | ||
| * 28 October 2021: Update outliers and broaden subsampling. ([7a2dba5](https://github.com/nextstrain/zika/commit/7a2dba5ac298e8edecacd5e19124399f713af33f)) | ||
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| ## 2020 | ||
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| * 13 December 2020: Update zika build to use `--output-node-data` instead of `--output`. ([4c47f43](https://github.com/nextstrain/zika/commit/4c47f439ba714cbf5e25a81462de2819ac16f9d0)) | ||
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| ## 2019 | ||
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| * 14 December 2019: Add footer description to export. ([PR #11](https://github.com/nextstrain/zika/pull/11)) | ||
| * 10 December 2019: Switch to augur export v2. ([PR #10](https://github.com/nextstrain/zika/pull/10)) | ||
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| ## 2018 | ||
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| * 27 December 2018: Move vdb download call from python2 to python3. ([12d35b2](https://github.com/nextstrain/zika/commit/12d35b281fcb9b0482b58e1247dad2ee500e83b4)) | ||
| * 29 October 2018: Updates to Zika reference, dropped strains, min-length, and sampling bias correction. ([9e50fe2](https://github.com/nextstrain/zika/commit/9e50fe2dc6ac8209e829278007a938bba7ea7b32)) | ||
| * 06 July 2018: Attempt at streamlining the snakefile ([PR #8](https://github.com/nextstrain/zika/pull/8)) | ||
| * 29 June 2018: Travis CI configuration to run the example data build. ([5c4f6f6](https://github.com/nextstrain/zika/commit/5c4f6f6b682422f568280093d8548e7c77428d6f)) | ||
| * 29 June 2018: Download sequences from fauna automatically. ([ee8cc38](https://github.com/nextstrain/zika/commit/ee8cc38ff5ab46db2bd5f4ac136811bcead5f003)) | ||
| * 15 June 2018: Initial commit ([5640dba](https://github.com/nextstrain/zika/commit/5640dba33661365c0a9cf8614d2c04b01d227b15)) |