snakemake/snakemake-wrappers
Oct 2025 – Oct 2025
1 Month active
Languages Used
PythonShellYAML
Technical Skills
BioinformaticsData AnalysisNextflowPython ScriptingSnakemakeSoftware Packaging
Hamdiye Uzuner
PROFILE
Hamdiye Uzuner
Hamdiye Uzuner developed Orthanq integration wrappers for HLA and virus analyses within the snakemake-wrappers repository, enabling scalable and reproducible haplotype quantification workflows. She designed configuration files, metadata, and wrapper scripts in Python and Shell, ensuring Orthanq commands executed reliably for both viral and HLA contexts. By implementing end-to-end tests and correcting output paths for result files, Hamdiye improved the maintainability and reliability of the workflow. Her work focused on workflow management and software packaging, allowing seamless integration of Orthanq-driven analyses into existing Snakemake pipelines and supporting robust downstream data analysis in bioinformatics research environments.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
2Total
Bugs
0
Commits
2
Features
1
Lines of code
718
Activity Months1
Your Network
25 people
Work History
October 2025
2 Commits • 1 Features
Oct 1, 2025In October 2025, delivered Orthanq integration wrappers for HLA and virus analyses in snakemake-wrappers, including configuration files, metadata, test cases, and wrapper scripts to execute Orthanq commands for haplotype quantification in viral and HLA contexts. Also fixed the output path so Orthanq results (CSV) are written to the designated output folder. Implemented end-to-end tests to validate wrapper behavior, enhancing reproducibility and reliability. This work enables scalable, reproducible haplotype analysis and improves downstream analytics and decision-making within Snakemake pipelines.
2 Commits • 1 Features
Oct 1, 2025In October 2025, delivered Orthanq integration wrappers for HLA and virus analyses in snakemake-wrappers, including configuration files, metadata, test cases, and wrapper scripts to execute Orthanq commands for haplotype quantification in viral and HLA contexts. Also fixed the output path so Orthanq results (CSV) are written to the designated output folder. Implemented end-to-end tests to validate wrapper behavior, enhancing reproducibility and reliability. This work enables scalable, reproducible haplotype analysis and improves downstream analytics and decision-making within Snakemake pipelines.
October 2025
Activity
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Quality Metrics
Correctness100.0%
Maintainability100.0%
Architecture100.0%
Performance70.0%
AI Usage70.0%
Skills & Technologies
Programming Languages
PythonShellYAML
Technical Skills
BioinformaticsData AnalysisNextflowPython ScriptingSnakemakeSoftware PackagingTestingWorkflow Management
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