nf-core/modules
Nov 2024 – Jan 2026
5 Months active
Languages Used
GroovyPythonYAMLNextflow
Technical Skills
BioinformaticsData AnalysisNextflowPython ScriptingData ProcessingWorkflow Development
Chao-Jen Wong
PROFILE
Chao-jen Wong
Over five months, contributed to the nf-core/modules repository by developing and enhancing bioinformatics workflow modules using Nextflow, Python, and Groovy. Delivered features such as AnnData subsetting by barcode, Cellbender empty droplet removal, and CNV calling for PacBio HiFi data, each with integrated testing and documentation to ensure reproducibility and maintainability. Upgraded container security by standardizing HTTPS references and improved output formats, including phased BAM emission and optional data outputs in Sawfish. Focused on robust data processing, workflow reliability, and cross-team collaboration, consistently aligning with nf-core standards while expanding test coverage and supporting evolving genomics analysis requirements.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
7Total
Bugs
0
Commits
7
Features
6
Lines of code
1,436
Activity Months5
Your Network
182 peopleSame Organization
@seattlechildrens.org2
Work History
January 2026
1 Commits • 1 Features
Jan 1, 2026January 2026 — nf-core/modules delivered a flexible option for emission of genome.gclevels.mpack in the Sawfish discover process, enabling configurable data output without breaking downstream validation. The feature was shipped with updated tests and validation logic to reflect the new behavior, reducing false negatives and ensuring more robust data presence checks. Collaboration with the SP Pearce team completed the change, with co-authored commits and alignment to nf-core testing standards.
1 Commits • 1 Features
Jan 1, 2026January 2026 — nf-core/modules delivered a flexible option for emission of genome.gclevels.mpack in the Sawfish discover process, enabling configurable data output without breaking downstream validation. The feature was shipped with updated tests and validation logic to reflect the new behavior, reducing false negatives and ensuring more robust data presence checks. Collaboration with the SP Pearce team completed the change, with co-authored commits and alignment to nf-core testing standards.
January 2026
December 2025
1 Commits • 1 Features
Dec 1, 2025December 2025 monthly summary for nf-core/modules: Key feature delivered is the Hiphase Module 1.5.0 release with phased BAM emission, plus quality improvements and better testing alignment. No major bugs reported; focus was on feature delivery, output enhancements, and release QA. Overall impact: enables phased BAM-based analyses in pipelines, improves output clarity and compatibility with downstream tools, and strengthens release quality through updated test snapshots. Technologies/skills demonstrated: semantic versioning, release orchestration, integration with wave container, output schema updates, and test snapshot maintenance.
December 2025
1 Commits • 1 Features
Dec 1, 2025December 2025 monthly summary for nf-core/modules: Key feature delivered is the Hiphase Module 1.5.0 release with phased BAM emission, plus quality improvements and better testing alignment. No major bugs reported; focus was on feature delivery, output enhancements, and release QA. Overall impact: enables phased BAM-based analyses in pipelines, improves output clarity and compatibility with downstream tools, and strengthens release quality through updated test snapshots. Technologies/skills demonstrated: semantic versioning, release orchestration, integration with wave container, output schema updates, and test snapshot maintenance.
November 2025
3 Commits • 2 Features
Nov 1, 2025November 2025 monthly summary for nf-core/modules focusing on the PacBio HiFi CNV calling expansion and container security improvements.
3 Commits • 2 Features
Nov 1, 2025November 2025 monthly summary for nf-core/modules focusing on the PacBio HiFi CNV calling expansion and container security improvements.
November 2025
December 2024
1 Commits • 1 Features
Dec 1, 2024December 2024 monthly work summary for nf-core/modules focused on feature delivery and code quality improvements. Delivered a new Cellbender Empty Droplet Removal Subworkflow, integrated Cellbender and Anndata modules, refined outputs, added tests, and renamed the subworkflow for clarity and linting compliance. No major bugs fixed this month; effort centered on reliability, test coverage, and maintainability.
December 2024
1 Commits • 1 Features
Dec 1, 2024December 2024 monthly work summary for nf-core/modules focused on feature delivery and code quality improvements. Delivered a new Cellbender Empty Droplet Removal Subworkflow, integrated Cellbender and Anndata modules, refined outputs, added tests, and renamed the subworkflow for clarity and linting compliance. No major bugs fixed this month; effort centered on reliability, test coverage, and maintainability.
November 2024
1 Commits • 1 Features
Nov 1, 2024November 2024 performance summary for nf-core/modules: Delivered a new Nextflow module to subset AnnData objects by barcode list, enhancing reproducibility and workflow efficiency. This feature enables precise cell filtering via Python/anndata, writes results to a new H5AD file, and includes testing and version-tracking to ensure stability across releases. No major bugs reported this month; ongoing validation and documentation updates supported adoption across teams.
1 Commits • 1 Features
Nov 1, 2024November 2024 performance summary for nf-core/modules: Delivered a new Nextflow module to subset AnnData objects by barcode list, enhancing reproducibility and workflow efficiency. This feature enables precise cell filtering via Python/anndata, writes results to a new H5AD file, and includes testing and version-tracking to ensure stability across releases. No major bugs reported this month; ongoing validation and documentation updates supported adoption across teams.
November 2024
Activity
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Quality Metrics
Correctness91.4%
Maintainability88.6%
Architecture88.6%
Performance82.8%
AI Usage34.2%
Skills & Technologies
Programming Languages
GroovyNextflowPythonYAML
Technical Skills
BioinformaticsData AnalysisData ProcessingNextflowPython ScriptingWorkflow Developmentbioinformaticscondacontainerizationdata analysisdata processinggenomicsnextflow
Repositories Contributed To
Overview of all repositories you've contributed to across your timeline