mskcc-omics-workflows/modules
Mar 2025 – Mar 2025
1 Month active
Languages Used
GroovyJSONN/ANextflowPython
Technical Skills
BioinformaticsCI/CDGenomicsNextflowScriptingTesting
John Orgera
PROFILE
John Orgera
John Orgera contributed to the mskcc-omics-workflows/modules repository by standardizing neoantigen input and output naming conventions, refactoring Nextflow scripts to enforce consistent _input.json suffixes and updating associated tests to preserve data provenance. He 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. John also refreshed test artifacts, removed obsolete snapshots, and updated test infrastructure to align with newer Nextflow tooling. His work leveraged skills in bioinformatics, workflow management, and scripting with Python and Groovy, demonstrating careful attention to reproducibility and maintainability in genomics pipelines.
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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