September 2025 monthly summary for hartwigmedical/scripts focusing on pipeline improvements, release readiness, and maintainability.

Monthly Summary for 2025-08 focusing on delivery, quality, and impact of work on hartwigmedical/scripts. The major delivery this month was the WGS Metrics Workflow updated for multi-metric support across Illumina, Ultima, and SBX, with new stages and refactored input handling and resource configurations to support multiple metric collection types, significantly improving robustness and reusability. No separate major bugs were reported in this period; stability was enhanced through refactoring and tighter input/resource management. The changes position the workflow for easier extension to additional metric types in future releases.

Month: 2025-07 — Performance-focused update to the hartwigmedical/scripts WGS metrics workflows. Delivered configurable, multi-stage WGS metrics capabilities and an HG19 end-to-end workflow definition, with containerized deployment. No explicit bug fixes recorded this period. Business impact includes greater analysis granularity, improved reproducibility, and streamlined deployment for WGS data processing across samples and references.

June 2025 — hartwigmedical/scripts: Delivered an end-to-end WGS metrics workflow using GATK CollectWgsMetrics, configured via YAML, with environment setup and BAM processing steps. Enhanced to support a flexible Docker image and introduced a simplified gatk.sh script (v0.0.5). Fixed a typo in the workflow configuration that could disrupt command execution. These changes improve reproducibility, portability, and reliability of WGS quality control for downstream analyses.

2025-05 Monthly Summary: Delivered a feature update in hartwigmedical/scripts to QC plots by expanding the driver gene set used in sample report generation. This enhancement increases coverage for deletions in both the main QC report and the deamination-specific QC report, improving QC accuracy and reliability for sample-level decisions. No bugs were reported this month.

April 2025 monthly highlights for hartwigmedical/scripts focused on delivering two targeted features that strengthen CI/CD reliability and reporting quality. Key features delivered: - Workflow Version Bumps in YAML Generators: Bumped workflow references in genReconCnvYaml.py from 1.1.2 to 1.1.4 and in genSageVisYaml.py from 0.1.7 to 0.1.8 to align CI/CD with current standards, reducing deployment risk and improving reproducibility. (Commit: 197ea5e1e6cf6ae0fae80702297a390a5458cfa7) - Somatic Variant Reporting Enhancement: PON-filtered Gene Filtering: Enhanced reporting by passing PON-filtered variants within selected genes and refined VCF generation with gene-based filtering and PON artifact identification. (Commit: ab78744b7c0d757e20836daa464e891fe0952e0b) Major bugs fixed: - No major bugs recorded this month; efforts focused on feature delivery and CI/CD alignment. Overall impact and accomplishments: - Improved CI/CD reliability and reproducibility through version bumps in YAML generators, enabling smoother deployments. - Increased reporting accuracy and downstream analysis quality by incorporating PON-filtered variants and gene-based VCF filtering with PON artifact detection. - Clear traceability of changes via commit-level documentation, supporting faster audits and onboarding. Technologies/skills demonstrated: - Python scripting and YAML-based configuration (genReconCnvYaml.py, genSageVisYaml.py) - CI/CD concepts and version management - Somatic variant analysis concepts including PON filtering, gene-based filtering, and VCF generation - Change traceability and documentation for auditability

February 2025 — hartwigmedical/scripts: Delivered two critical updates to improve deployment reliability and tooling alignment. (1) Panel Workflow Version Upgrade: Bumped the panel workflow version in the generated YAML to the latest defined version to ensure reconcnv runs with up-to-date workflow logic (commit a084878d2287fddba50a26b7f7071edfcd673897). (2) ProjectX Toolset Update to 0.27.0: Updated Docker images to 0.27.0-d7c6b75, added metrics-alignment-metrics-rc and metrics-alignment-metrics-gdc, and removed read_collapser (commit 5406cb64751cbfa0491cad4a67b5e03765594e21). Overall impact: increased configuration correctness, enhanced observability, and readiness for Round 3 deployments. Technologies/skills demonstrated: YAML/config management, Docker image versioning, and CI/CD pipeline maintenance.

Month: 2024-11 — Performance summary for hartwigmedical/pipeline5. Focused on delivering reliable test coverage updates and safer VM lifecycle controls, aligning with business goals of robust CI/CD and cost-efficient resource management.