Over a three-month period, contributed to the EBI-Metagenomics/nf-modules repository by developing four features and resolving a critical bug, focusing on bioinformatics pipeline enhancements. Built and stabilized modules for CAZyme annotation and assembly decontamination, leveraging Nextflow, Bash, and Groovy to improve workflow reproducibility and data quality. Introduced new nf-core modules for BLAST and SeqKit, enabling flexible contaminant removal and streamlined reference data handling. Refactored alignment filtering to prioritize percentage identity and optimized Minimap2 settings for better performance. Emphasized robust testing, configuration management, and containerization, ensuring reliable, modular pipelines that support scalable metagenomics analyses and reproducible research outcomes.
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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