May 2026 monthly summary: Focused on delivering user-facing features, reliability improvements, and data-processing optimizations across hmftools and scripts. Key work included robust plotting fixes, a new prediction-output customization option, expanded cohort tooling, documentation enhancements, and streamlined genomic data handling to improve accuracy, reproducibility, and business value.

April 2026 monthly summary for hartwigmedical repositories — hmftools and scripts. Focused on data quality, reproducibility, deployment readiness, and user experience. Delivered a set of feature changes across Qsee/BQR/datasets, plot readability, README improvements, containerization, and script refactors. Minor bug fix included for -version output in fastq-tools. These efforts increase production confidence, reduce setup confusion, and enable faster iteration.

March 2026 monthly performance summary for hartwigmedical/hmftools and hartwigmedical/scripts focusing on business value and technical outcomes. The month delivered visible improvements in data visualization, build stability, deployment readiness, and path resolution across multiple projects, underpinned by a clear commit trail. Highlights include UI/plot enhancements for data clarity, dependency and version management to streamline builds, robust directory path handling for multi-project data, and Oncoanalysers pipeline resource scaffolding.

February 2026 monthly summary for hmftools and Qsee initiatives focused on stability, visualization, data-prep resilience, and deployment readiness. Key features delivered and major bug fixes improved business-critical dashboards, data workflows, and developer ergonomics across hmftools and the Qsee ecosystem. The month also saw substantial refactoring to support scalable QC and configurable thresholds, enabling faster iteration and safer deployments.

February 2026 monthly summary for 2026-01 (Hartwig Medical: hmftools). This period delivered core feature enhancements, extensive test coverage, and stability improvements across the hmftools suite, with a strong focus on data loading robustness and business-value outcomes. Key outcomes included the launch of Image Comparison Core with CUPPA support, introducing a renaming of the image data model to ComparableImage, and unit tests that validate image loading and CUPPA paths. These changes enhance reproducibility of image-based analyses and reduce load-time failures in production pipelines.

Month: 2025-12 — Hartwig Medical hmftools: concise monthly summary focused on delivering business value through feature delivery, reliability improvements, and documentation updates. Key items and outcomes: Key features delivered: - Cuppa: Removed PURPLE QC file dependency and switched to direct reading of PURPLE purity data, simplifying input requirements and improving user workflow for processing samples. This reduces setup steps and potential file-format errors. Commits: 18a56fb8bb23973c4fa356e49a76bac3b0c9e921; dde9c0241c6b270251ba1f0331d1b5b4dd1c88c9. - Cuppa: RNA sample ID handling — allows specifying different RNA sample IDs during processing and includes documentation updates clarifying input requirements, increasing flexibility when handling RNA alongside DNA data. Commits: f06add44013a30233c0a700b8377fbbb9f8ab9a9; 1e2d0e0647f49b8e3cf23c138fc6530a3fbcfbba. Major bugs fixed: - Logging: Improve error handling by routing exceptions directly to the logger instead of printing stack traces, enhancing logging clarity and consistency and improving supportability. Commit: de9a4693385eb05b4d7aa6d92b764aac2df2f57f. Overall impact and accomplishments: - Reduced input dependencies and streamlined workflows, enabling faster sample processing and fewer configuration errors. - Increased flexibility in data processing with RNA sample ID handling, improving multi-omics workflows. - Enhanced observability and maintainability through improved logging, aiding faster issue diagnosis and support. Technologies/skills demonstrated: - Python-based feature development and refactoring - Robust logging practices and error handling - Documentation improvements and input guidance - Change management and traceability via commit discipline

November 2025 performance summary for hartwigmedical/hmftools focused on delivering a cohesive set of refactors, percentile analytics enhancements, and end-to-end plotting readiness that directly improve reliability, speed-to-insight, and business value. Key architectural changes modernized feature modeling and testing, while the Cohort Percentiles pipeline was reworked for stability and clearer data output. The startup workflow now runs prep and plotting automatically, enabling faster, repeatable reporting with improved observability.

October 2025 performance summary focused on delivering business value through resource optimization, visualization accuracy, and developer-facing documentation across two repositories. Implemented resource packaging improvements for OncoAnalyser to reduce download size and simplify versioning, enhanced Linx visualizations for more accurate interpretation of results, and refreshed Lilac documentation to clarify algorithmic details and performance considerations.

September 2025 Monthly Summary: The period delivered impactful improvements across virus data build, CNV visualization, and Circos rendering, enhancing data completeness, traceability, and performance. Key features and robustness were achieved through targeted refactors, new data integrations, and optimized loading paths. Key features delivered: - VirusBreakend Database Build Enhancements (HPV33 genome and host sequence integration) in hartwigmedical/scripts; group commits 96dd1d00... and 004af284... restored HPV33 genome, fixed missing human sequence data, and updated build metadata and cloud storage paths. - SvVisualiser: Refactor Plot Modes and Enhanced Logging in hartwigmedical/hmftools; plot mode logic moved to private methods with unique file identifiers in logs (commits 9acd08d3...; 3510fc70...). - Linx Visualiser: CNV Plotting Enhancements and LINX Logging; default CNV plotting from driver data, CNV status included in circos file names, HET_DEL support, and improved sample data loading logs (commits 55d95601...; 97250b2e...; 8850b973...; 3db15384...). - Circos Output Improvements: File naming and conditional display of AMBER/COBALT tracks when directories are provided (commits 325162d8...; df7a99ad...). - Circos: AMBER Track Radius Bug Fix; Centromere Display Bug Fix; Linx Visualiser PURPLE Catalog Loading Optimization; improved rendering accuracy and data integrity (commits 5253e1e9...; 3f8a6d47...; d4a0f239...). Major bugs fixed: - Circos: AMBER Track outer radius calculation corrected (AMBER track positioning). - Circos: Centromere rendering fixed by passing correct reference genome version to loadConfigFile. Overall impact and accomplishments: - Improved data completeness and reliability for virusdb, enabling more accurate downstream analyses and surveillance. - Enhanced traceability and debugging across visualization tools with structured plotting modes and per-file identifiers. - Significant UI/data pipeline reliability gains from CNV plotting defaults, improved logging, and optimized PURPLE catalog loading. - Faster, more robust Circos outputs with consistent file naming and display behavior, reducing manual intervention and re-runs. Technologies/skills demonstrated: - Python refactoring and modularization; improved logging and traceability; data integration for HPV33 and host sequences. - Visualization tooling enhancements (SvVisualiser, LInx Visualiser) including default plotting, CNV visualization, HET_DEL support, and improved data loading logs. - Circos pipeline improvements: output naming conventions, conditional track rendering, and bug fixes; performance optimizations for catalog loading (PURPLE). - Cloud storage path management and build metadata updates for reproducibility.

August 2025 monthly summary for hartwigmedical/hmftools: Documentation improvements for Lilac project and LILAC tool focusing on user accessibility, onboarding, and maintainability. Key changes include removing outdated known-issues notes and restructuring README with clearer usage instructions, publication links, and sample/reference data. This work reduces user confusion, improves reproducibility, and lays groundwork for future enhancements.

July 2025 monthly performance summary highlighting delivery of reliability, traceability, and maintainability improvements across hmftools and scripts, with clear business value for data pipelines, visualization, and resource management. The month focused on improving observability, ensuring robust data outputs, aligning documentation with actual data structures, and streamlining resource configurations for reproducible builds.

June 2025: Delivered containerized deployments for critical pipelines, improved visualization reliability and performance, hardened data handling, and automated resource packaging and documentation alignment across hmftools and scripts. The work enhances deployability, stability, and developer productivity while delivering measurable business value to genomics workflows and Oncoanalyser resource management.

May 2025 performance summary for hartwigmedical/hmftools focusing on Linx visualization and Circos data pipelines. Delivered robust data loading, interpolation, and circos visualization for Cobalt ratios and Amber BAFs, underpinned by a core refactor of Linx and Circos data organization. Implemented plotting enhancements for per-gene views, GC ratio plotting, centromere highlighting, and Amber BAF lines, with optional fragile-site highlighting. Strengthened data robustness and production readiness through input validation improvements, chromosome range handling, and utility enhancements (PurpleSegment, Lilac, and Docker image improvements).

April 2025 highlights: The hmftools team delivered notable features and fixes across Orange WGS, Lilac allele filtering, NucleotideGeneEnrichment, and CHORD, delivering clear business value and improved robustness. Key outcomes include configurable WGS inputs, enhanced allele filtering accuracy and diagnostics, maintainable per-gene boundary mappings for variant processing, and strengthened MNV handling with better test coverage. The work reduces pipeline fragility, accelerates issue diagnosis, and supports scalable WGS configurations for diverse workflows.

Concise monthly summary for March 2025 focusing on business value and technical achievements in hartwigmedical/hmftools. Delivered reliability improvements, feature support for RNA data, and clarity in the scoring pipeline, enhancing decision support and reproducibility for top-ranked solutions.

February 2025 (2025-02) monthly summary for hartwigmedical/hmftools. Delivered feature enhancements, robustness improvements, and release readiness across docs, CI/CD, and data processing. Business value targeted improvements in user guidance, release processes, and data quality; major boosts in indel driver accuracy and VCF handling reliability.

January 2025 monthly summary for hartwigmedical/hmftools. Focused delivery across three key features with measurable improvements in scoring accuracy, deployment usability, and data presentation. No major bugs fixed documented this period. Overall impact includes improved decision support accuracy, streamlined HPC container workflows, and a clearer, more maintainable codebase.

December 2024 hmftools monthly summary focusing on reliability, onboarding, and scalable analysis capabilities. Delivered robust bug fixes, documentation enhancements, and features that improve reproducibility, plotting performance for large multi-sample workflows, and user guidance for Oncoanalyser pipelines.

November 2024 monthly summary for hartwigmedical repositories. Focused on expanding Java/OpenJDK compatibility, stabilizing CHORD workflows, and improving deployment hygiene and documentation. Key outcomes include cross-module OpenJDK 8-17 compatibility (Redux, Sage, Esvee; Sage >=9), parsing Sage version in VCF, and packaging improvements unifying run script and jar. Major CHORD work modernized the pipeline by migrating from R package to a script, introducing ChordModel and ChordApplication, adding end-to-end tests and improved output path handling, and cleaning up embedded components. Infra and packaging hygiene were improved with Dockerfiles for Cider, Peach, Teal, and Neo, and cleanup of obsolete circos base images and unnecessary Dockerfiles. Several stability fixes were delivered, including heatmap alignment correction, improved logging for Sage errors, and enhanced release-detection regex; these changes reduce deployment risk and support easier CI/CD. Documentation was updated for Oncoanalyser and CHORD/readme to improve onboarding and usage.

Consolidated Infra and packaging improvements for hmftools in October 2024, delivering cross-component OncoAnalyser requirements, Circos installation/configuration, micromamba-based environments with sambamba, and standardized Dockerfiles, along with targeted bug fixes to improve reliability, CI resilience, and tooling accuracy. These changes bolster reproducibility, reduce onboarding time, and enable smoother data analysis pipelines using OncoAnalyser across Lilac, Orange, Sigs, Virusinterpreter, and Sage.