All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- Initial pipeline: pixi-managed environment, dorado 2.1.2 install with a config-resolved model stack (ONT simplex + modified-base models, plus local custom models), per-sample / per-barcoded-run basecalling with resume, MinKNOW-basecalled input, dorado or minimap2 alignment, modkit pileup / summary / extract / bigWig / DMR, samtools + mosdepth QC, a per-project summary table, optional DNAscent (index, detect, per-read BrdU/EdU table, forkSense), config-driven custom steps, Bodhi and Alpine Slurm profiles, unit tests and CI.
- Documentation site (zensical, GitHub Pages) with an installation guide, a step-by-step walkthrough from a POD5 run directory to modification calls, and user-guide pages for the samples file, configuration, models, running, and outputs; the README now points at it.