From b5c6d10813eabdab99af835168544c2d2f7a2879 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Mon, 26 Feb 2024 11:46:44 -0800 Subject: [PATCH] Add CHANGELOG --- CHANGELOG.md | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 CHANGELOG.md diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..c67c87d --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,50 @@ +# CHANGELOG + +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. + +## 2024 + +* 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). + +## 2023 + +* 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) + +## 2022 + +* 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) + +## 2021 + +* 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) + +## 2020 + +* 13 December 2020: Update zika build to use `--output-node-data` instead of `--output`. (4c47f439ba714cbf5e25a81462de2819ac16f9d0) + +## 2019 + +* 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) + +## 2018 + +* 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. \ No newline at end of file