mskcc-omics-workflows/modules
Mar 2025 – Mar 2025
1 Month active
Languages Used
GroovyJSONN/ANextflowPython
Technical Skills
BioinformaticsCI/CDGenomicsNextflowScriptingTesting
John Orgera
PROFILE
John Orgera
Worked on the mskcc-omics-workflows/modules repository to enhance the reliability and standardization of genomics workflows. Focused on refining the neoantigen input process by enforcing a consistent _input.json naming convention, which involved refactoring Nextflow scripts and updating associated tests to maintain data provenance and reduce downstream errors. Improved the accuracy of Non-sense Mediated Decay calculations by correcting position indexing and mutation-distance logic relative to exon boundaries, addressing edge-case prediction reliability. Updated test artifacts and infrastructure to align with new output conventions and Nextflow tooling versions, leveraging skills in bioinformatics, scripting, and CI/CD to ensure reproducibility and workflow integrity.
Overall Statistics
Feature vs Bugs
67%Features
Repository Contributions
6Total
Bugs
1
Commits
6
Features
2
Lines of code
323
Activity Months1
Your Network
8 peopleShared Repositories
8
buehlereMember
EricWilliam BuehlerMember
mikefeixuMember
Yu HuMember
Nikhil KumarMember
John OrgeraMember
Ronak ShahMember
“FeiMember
Work History
March 2025
6 Commits • 2 Features
Mar 1, 2025March 2025 monthly summary for the mskcc-omics-workflows/modules repository, focusing on business value, technical achievements, and readiness for broader adoption. Highlights include standardization of outputs, accuracy improvements in core calculations, and aligned test artifacts to ensure reliability across Nextflow tooling.
6 Commits • 2 Features
Mar 1, 2025March 2025 monthly summary for the mskcc-omics-workflows/modules repository, focusing on business value, technical achievements, and readiness for broader adoption. Highlights include standardization of outputs, accuracy improvements in core calculations, and aligned test artifacts to ensure reliability across Nextflow tooling.
March 2025
Activity
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Quality Metrics
Correctness86.6%
Maintainability90.0%
Architecture83.4%
Performance93.4%
AI Usage20.0%
Skills & Technologies
Programming Languages
GroovyJSONN/ANextflowPython
Technical Skills
BioinformaticsCI/CDGenomicsNextflowScriptingTestingWorkflow Management
Repositories Contributed To
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