Mattock contributed to the EBI-Metagenomics/nf-modules repository by developing and refining bioinformatics workflows for metagenomics analysis. Over three months, he built new Nextflow modules for CAZyme annotation, sequence alignment, and sequence filtering, and implemented an assembly decontamination subworkflow to improve data quality and reproducibility. His work involved optimizing pipeline modularity and performance, including refactoring alignment filtering to prioritize percentage identity and tuning Minimap2 for faster processing. Using Bash, Groovy, and YAML, Mattock ensured robust environment management, comprehensive testing, and seamless integration of new features, demonstrating depth in pipeline development and a strong focus on maintainable, reliable workflows.
May 2025: Delivered a high-impact feature in nf-modules that re-prioritized alignment filtering to PID over MAPQ and tuned Minimap2 for performance. Updated defaults and tests to reflect the change, improving downstream analysis accuracy and processing throughput while maintaining compatibility with existing workflows.
May 2025: Delivered a high-impact feature in nf-modules that re-prioritized alignment filtering to PID over MAPQ and tuned Minimap2 for performance. Updated defaults and tests to reflect the change, improving downstream analysis accuracy and processing throughput while maintaining compatibility with existing workflows.
For 2025-03, delivered two new nf-core modules and a new assembly decontamination subworkflow in EBI-Metagenomics/nf-modules. The work strengthens pipeline modularity, data quality, and reproducibility for metagenomics workflows. Key outcomes include the introduction of BLAST_BLASTN and SEQKIT_GREP modules, a new assembly decontamination subworkflow leveraging BLAST and SeqKit to identify and remove contaminants against a reference genome, configurable reference data handling, robust input pipelines, and comprehensive tests. Stability improvements were made, including removing use of blast_reference_genomes_folder, adding blastdb path support, and enhancing nf-test contig checks, which reduce manual adjustments and improve reliability across releases.
For 2025-03, delivered two new nf-core modules and a new assembly decontamination subworkflow in EBI-Metagenomics/nf-modules. The work strengthens pipeline modularity, data quality, and reproducibility for metagenomics workflows. Key outcomes include the introduction of BLAST_BLASTN and SEQKIT_GREP modules, a new assembly decontamination subworkflow leveraging BLAST and SeqKit to identify and remove contaminants against a reference genome, configurable reference data handling, robust input pipelines, and comprehensive tests. Stability improvements were made, including removing use of blast_reference_genomes_folder, adding blastdb path support, and enhancing nf-test contig checks, which reduce manual adjustments and improve reliability across releases.
February 2025 focused on delivering a CAZyme annotation capability via the DBCAN module in the nf-modules repository, and hardening the DBCAN test suite to ensure reliable, version-aware CI pipelines. These efforts improve CAZyme annotation workflows for proteins, boost reproducibility, and set the stage for future module expansions.
February 2025 focused on delivering a CAZyme annotation capability via the DBCAN module in the nf-modules repository, and hardening the DBCAN test suite to ensure reliable, version-aware CI pipelines. These efforts improve CAZyme annotation workflows for proteins, boost reproducibility, and set the stage for future module expansions.
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