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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 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, in that this is a new feature to pulling data from NCBI datasets and perform subsequent curation, instead of relying on the `fauna` database. The subsequent restructuring of the `phylogenetic` pipeline into its own directory keeps the two workflows modular and better conforms to the [pathogen repo guide](https://github.com/nextstrain/pathogen-repo-guide). | ||
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| ## 2023 | ||
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| * 04 May 2024: 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. (7a2dba5ac298e8edecacd5e19124399f713af33f) | ||
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| ## 2020 | ||
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| * 13 December 2020: Update zika build to use `--output-node-data` instead of `--output`. (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 2029: 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. (12d35b281fcb9b0482b58e1247dad2ee500e83b4) | ||
| * 29 Oct 2018: Updates to Zika reference, dropped strains, min-length, and sampling bias correction. (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. (5c4f6f6b682422f568280093d8548e7c77428d6f) | ||
| * 29 June 2018: Download sequences from fauna automatically. (ee8cc38ff5ab46db2bd5f4ac136811bcead5f003) | ||
| * 15 June 2018: Initial commit. |