mskcc-omics-workflows/modules
Dec 2024 – Feb 2025
2 Months active
Languages Used
GroovyN/AYAMLnfJSONNextflowPythonShell
Technical Skills
CI/CDDevOpsTestingWorkflow DevelopmentWorkflow Managementnextflow
John Orgera
PROFILE
John Orgera
Raj Orge contributed to the mskcc-omics-workflows/modules repository by enhancing neoantigen input pipelines and standardizing module parameters to improve clarity and reliability. He integrated Ensembl annotation data, enabling more accurate genomic predictions, and implemented configurable kD cutoffs with improved mutation and frameshift detection. Raj updated test suites and CI/CD workflows using Nextflow, Python, and GitHub Actions, ensuring compatibility with evolving tool versions and reducing maintenance overhead. His work focused on robust workflow development, aligning cross-module APIs, and automating testing, which streamlined deployment processes and improved end-to-end accuracy for genomic data processing pipelines within a short two-month period.
Overall Statistics
Feature vs Bugs
80%Features
Repository Contributions
19Total
Bugs
1
Commits
19
Features
4
Lines of code
1,135
Activity Months2
Your Network
15 people
Work History
February 2025
13 Commits • 3 Features
Feb 1, 2025February 2025 monthly summary for mskcc-omics-workflows/modules: Focused on delivering robust Neoantigen input pipeline enhancements, Ensembl annotation integration, and CI/CD improvements. These changes increased prediction accuracy, reliability, and deployment velocity, delivering measurable business value.
13 Commits • 3 Features
Feb 1, 2025February 2025 monthly summary for mskcc-omics-workflows/modules: Focused on delivering robust Neoantigen input pipeline enhancements, Ensembl annotation integration, and CI/CD improvements. These changes increased prediction accuracy, reliability, and deployment velocity, delivering measurable business value.
February 2025
December 2024
6 Commits • 1 Features
Dec 1, 2024Month 2024-12: Consolidated API clarity and pipeline reliability in mskcc-omics-workflows/modules. Delivered cross-module parameter standardization (rename typePan to fromPan) across NETMHCPAN4, netmhc3, and netmhcstabpan; updated tests accordingly. In parallel, fixed CI/test stability by updating snapshots and CI installation to align with newer nf-test and Nextflow versions, ensuring reliable test results going forward. These efforts reduce onboarding friction, lower risk in production deployments, and improve maintainability across the repository.
December 2024
6 Commits • 1 Features
Dec 1, 2024Month 2024-12: Consolidated API clarity and pipeline reliability in mskcc-omics-workflows/modules. Delivered cross-module parameter standardization (rename typePan to fromPan) across NETMHCPAN4, netmhc3, and netmhcstabpan; updated tests accordingly. In parallel, fixed CI/test stability by updating snapshots and CI installation to align with newer nf-test and Nextflow versions, ensuring reliable test results going forward. These efforts reduce onboarding friction, lower risk in production deployments, and improve maintainability across the repository.
Activity
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Quality Metrics
Correctness86.4%
Maintainability87.2%
Architecture81.0%
Performance79.0%
AI Usage20.0%
Skills & Technologies
Programming Languages
GroovyJSONN/ANextflowPythonShellYAMLnf
Technical Skills
BioinformaticsCI/CDCommand Line InterfaceData FilteringData ProcessingDevOpsGenomic Data ProcessingGenomicsGitHub ActionsNextflowNextflow ScriptingPipeline DevelopmentPython ScriptingScriptingTesting
Repositories Contributed To
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