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Changelog

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.

[0.3.0] - 2026-03-08

Added

  • Support for Long-Read (LR) sequencing data (e.g., Oxford Nanopore) using minimap2 for alignment and indexing.
  • Configurable READ_TYPE parameter (NGS vs LR) and SCORE_RATIO_CUTOFF in config.yaml.
  • Refined co-infection detection logic using clade information from NextStrain.tsv to improve accuracy for long-read data.

Changed

  • Updated Mapping.py and RSV_functions.py to handle single-end reads gracefully during QC and read binning.

[0.2.1] - 2026-03-07

Changed

  • Modernized PDF and HTML report formats with a professional card-based layout and improved CSS.
  • Enhanced visual hierarchy in reports using slate-blue color schemes and responsive design.

[0.2.0] - 2026-03-07

Added

  • Co-infection detection logic to identify multiple RSV strains (different subtypes or clades) in a single sample.
  • Automated read binning using BWA and Samtools to separate co-infection components into distinct read sets.
  • Component-specific assembly and genotyping pipelines, creating separate output directories (e.g., -comp1, -comp2).
  • Real-time console notifications in the main pipeline when co-infections are identified.
  • Highlighted and styled co-infection notifications in individual sample report sections.

Changed

  • Enhanced visual hierarchy in reports using slate-blue color schemes and responsive design.
  • Refactored Mapping.py to support multi-component processing and standardized read naming.
  • Updated Report_functions.py to correctly identify references and subtypes for co-infection components by inspecting the reference directory.
  • Silenced IQTREE3 STDOUT by redirecting output to log files to keep the terminal output clean.
  • Updated tree builder from FastTree to IQtree3 for more accurate phylogenetic analysis.
  • Updated the QC calling function (qc_call) for more nuanced quality assessment.
  • Improved PDF and HTML reports with more detailed QC status in summary tables.
  • Refined QC calling logic to provide more concise "Good" status messages.
  • Optimized PDF summary table column widths to prevent clipping and ensure all data fits within page margins.

Fixed

  • Resolved NameError in Mapping.py related to KMA logging variables.
  • Resolved FileNotFoundError in reporting when processing co-infection components that utilized different reference genomes.
  • Resolved ValueError in percentage formatting for the QC rate column in reports.
  • Fixed logic to hide co-infection notifications for single-infection samples in the detailed report sections.

[0.1.2] - 2025-04-01

Changed

  • Updated the reference database for genotyping.
  • Removed G-protein based genotyping to remain consistent with current research standards. More details can be found in the Nextclade data repository changelog.

[0.1.1]

Added

  • Implemented a version control function to track pipeline and database versions.
  • Added two new mutations to the RSV-B F-protein mutation list: I64T+K65E and N208D.

[0.1.0]

Added

  • Initial release of the RSVrecon pipeline.