January 2026 (EBI-Metagenomics/nf-modules): Focused on ensuring pipeline compatibility and ongoing nf-modules reliability for CGC workflows. Key deliverable: Pipeline Compatibility Updates for CGC Subworkflow and nft-utils Plugin, with an updated CGC subworkflow snapshot to reflect new assembly sequences and Nextflow version changes, and an upgrade of the nft-utils plugin to maintain compatibility and availability (0.0.8). Key achievements: - Pipeline Compatibility Updates for CGC Subworkflow and nft-utils Plugin: updated subworkflow snapshot to reflect new assembly sequences and Nextflow changes; upgraded nft-utils plugin to 0.0.8. - Commit-level traceability: changes captured in two commits (cfeff30dbf938786d1f4c3af08b4261d1d7e508e; 4019e6463ddcb6ef09935cc11339200820863b14). Major bugs fixed: none reported this month; however, the updates address known compatibility gaps that could block downstream analyses, reducing potential runtime errors. Overall impact and business value: - Maintains reliability of nf-modules in current CGC workflows, enabling smooth downstream analyses and data processing pipelines. - Reduces risk of breakages due to assembly sequence changes and Nextflow version updates; ensures continued availability of nft-utils. Technologies/skills demonstrated: - Nextflow version handling and pipeline compatibility - Dependency and plugin management (nft-utils 0.0.8) - Git-based change tracking and commit hygiene - nf-modules maintenance and repository hygiene

October 2025: Focused on documenting and scoping the SeqSubmit automation initiative for nf-core/website. Delivered the SeqSubmit project description and outlined hackathon-driven goals to prototype nf-core subworkflows for assembly and MAG submissions. No major bugs fixed this month; work centered on documentation, planning, and establishing a solid foundation for automation. The efforts enhance data submission efficiency, contributor onboarding, and cross-team alignment, and demonstrate strong technical writing, project scoping, and nf-core ecosystem skills.

August 2025 - EBI-Metagenomics nf-modules: Strengthened testing for Assembly & Decontamination workflows and improved test data hygiene. Delivered new test datasets and indices, cleaned outdated data, and updated Nextflow workflow test references and snapshot tests to reflect current inputs and paths. These changes improve CI stability, reduce flaky tests, and accelerate safe feature validation.

July 2025: nf-modules stability improvements in the decontamination workflow. Delivered targeted bug fixes to input path handling and identity filtering, corrected a typographical error ('indentity' to 'identity') in FILTERPAF, and updated contaminant_reference handling to use file() to prevent runtime errors. These changes improve filtering accuracy, prevent misclassification of contaminants, and enhance pipeline reliability and reproducibility.

June 2025: Delivered a major overhaul of the decontamination workflow in the EBI-Metagenomics nf-modules, including input refactor to accept a tuple of contigs and reference genomes, switch to percentage-identity filtering, and renaming contaminant_genome to contaminant_reference for clearer semantics. These changes reduce ambiguity, improve maintainability, and enable broader reuse across pipelines.

May 2025 performance highlights for EBI-Metagenomics nf-modules: delivered a minimap2-based host decontamination subworkflow for contigs with integrated filterpaf, expanded testing for compressed inputs and new thresholds, and updated snapshots to reflect behavioral changes. Added the filterpaf module with YAML configuration, test data, and additional filtering parameters. Introduced version tracking (versions.yml) and ensured decontaminate_contigs emits version information from its constituent steps to improve reproducibility. Strengthened stability and governance through lint fixes, expanded test coverage, file-name collision safeguards, and plugin support. These changes collectively improve data quality by reducing host contamination, enhance reproducibility and auditability, and demonstrate robust testing and configuration management.

March 2025 performance summary for EBI-Metagenomics nf-modules. Delivered significant enhancements to Krona-based taxonomy visualization and integration, improved input handling for CATPACK_CONTIGS workflows, and updated gene-caller tooling to reflect the prodigal-to-pyrodigal migration. Strengthened test coverage and data stability across taxonomy and contigs pipelines, with updated test data and output naming to ensure reliable downstream analyses. These efforts reduce maintenance overhead, improve pipeline reliability, and enable more accurate taxonomic reporting and visualization for end users.

February 2025: Implemented a comprehensive end-to-end taxonomic classification workflow within EBI-Metagenomics nf-modules. Delivered the TAXONOMY/taxonomic_classification subworkflow that combines DIAMOND BLASTP and CATPACK CONTIGS to classify predicted proteins and contigs from metagenomic data. Added database preparation support, updated module paths, enhanced metadata, and organized tests to enable robust end-to-end taxonomic profiling. Performed refactors to align with nf-core conventions, updated Diamond input handling, and improved test scaffolding (nf-test).