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.
- 26 February 2024: Exclude circular synthetic (or chimeric) and duplicate sequences. PR #29
- 23 February 2024: Use nextclade v3 dataset to classify records into subtypes (DENV1/I, DENV1/II, DENV4/I, etc). PR #16
- 24 February 2024: Split the pair of metadata.tsv and sequences.fasta files by serotype (DENV1-DENV4) using NCBI
virus-tax-idfield. PR #20 - 09 January 2024: Use a phylogenetic directory to start conforming to the pathogen-repo-guide. PR #15
- 05 December 2023: Initialize the ingest directory for pulling data from NCBI datasets and subsequent curation for a single pair of metadata.tsv and sequences.fasta files. PR #13
- 12 October 2023: Since multiple records can have the same strain name, use the "accession" column as the ID column instead. PR #12
- 09 April 2023: Add the DENV2/AII clade amino acid defining changes. PR #11
- 13 October 2022: Instead of pulling data from the fauna database, pull data from an s3 url PR #5
- 05 April 2022: CI: Use a centralized pathogen repo CI workflow. PR #3
- 04 April 2022: Migrate CI to GitHub Actions. PR #3
- 09 November 2021: CI: Upgrade setuptools suite prior to installation. PR #2
- 10 December 2019: Switch to export v2. PR #1
- 16 August 2019: Update build to work with ViPR data. (https://github.com/nextstrain/dengue/commit/081f9f82d971e75848ac1967bf6d841e05428545)
- 30 December 2018: Initialize the dengue repository. (https://github.com/nextstrain/dengue/commit/3e0f9feaa4d1799cdda6cf839e03d09390f39c53)