snakemake/snakemake-wrappers
Sep 2025 – Feb 2026
3 Months active
Languages Used
PythonShellYAML
Technical Skills
BioinformaticsData ConversionPython ScriptingShell ScriptingSnakemakeVCF Processing
tdayris
PROFILE
Tdayris
Developed and delivered multiple genomics data processing wrappers for the snakemake/snakemake-wrappers repository, focusing on reproducible workflows and streamlined data conversion. Built new Snakemake wrappers for tasks such as Illumina SampleSheet format conversion, VCF reformatting, VCF to MAF transformation with Ensembl VEP integration, and effective genome size calculation from BAM files. Introduced a Go-yq wrapper to automate YAML and CSV processing, supporting concatenation, format conversion, and expression evaluation. Enhanced workflow management by implementing centralized path configuration for the GATK meta-wrapper using Python, Shell, and YAML, emphasizing test-driven development, reproducible environments, and maintainable, template-driven pipeline design.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
6Total
Bugs
0
Commits
6
Features
3
Lines of code
1,140
Activity Months3
Work History
February 2026
1 Commits • 1 Features
Feb 1, 2026February 2026: Delivered centralized path configuration for the GATK Meta-wrapper via the new pathvars syntax in snakemake-wrappers, with templated path placeholders for references, indexes, intervals, known variants, and inputs, plus updates to outputs and logs to reflect the configured layout. No major bugs fixed this month; primary focus on feature delivery and code quality. This work enhances reproducibility, reduces setup time, and simplifies maintenance across workflows. Demonstrated strong proficiency in Python, Snakemake, YAML templating, and test-driven development, while adhering to conventional commits.
1 Commits • 1 Features
Feb 1, 2026February 2026: Delivered centralized path configuration for the GATK Meta-wrapper via the new pathvars syntax in snakemake-wrappers, with templated path placeholders for references, indexes, intervals, known variants, and inputs, plus updates to outputs and logs to reflect the configured layout. No major bugs fixed this month; primary focus on feature delivery and code quality. This work enhances reproducibility, reduces setup time, and simplifies maintenance across workflows. Demonstrated strong proficiency in Python, Snakemake, YAML templating, and test-driven development, while adhering to conventional commits.
February 2026
December 2025
1 Commits • 1 Features
Dec 1, 2025December 2025 monthly summary for snakemake/snakemake-wrappers: Delivered a Go-yq YAML/CSV processing wrapper enabling concatenation, format conversion, content updates, expression evaluation, splitting, and automatic format detection/validation. Implemented end-to-end tests for concat, update, evaluate, split, and format-conversion scenarios. Added reproducible environment specifications and package metadata to ensure stable, reusable deployments. This work reduces manual data wrangling time, improves reproducibility, and expands the wrapper ecosystem for YAML/CSV pipelines.
December 2025
1 Commits • 1 Features
Dec 1, 2025December 2025 monthly summary for snakemake/snakemake-wrappers: Delivered a Go-yq YAML/CSV processing wrapper enabling concatenation, format conversion, content updates, expression evaluation, splitting, and automatic format detection/validation. Implemented end-to-end tests for concat, update, evaluate, split, and format-conversion scenarios. Added reproducible environment specifications and package metadata to ensure stable, reusable deployments. This work reduces manual data wrangling time, improves reproducibility, and expands the wrapper ecosystem for YAML/CSV pipelines.
September 2025
4 Commits • 1 Features
Sep 1, 2025In September 2025, delivered a set of new genomics-focused Snakemake wrappers in the snakemake-wrappers repository, expanding end-to-end data processing capabilities and enabling reproducible pipelines for large-scale genomics workloads.
4 Commits • 1 Features
Sep 1, 2025In September 2025, delivered a set of new genomics-focused Snakemake wrappers in the snakemake-wrappers repository, expanding end-to-end data processing capabilities and enabling reproducible pipelines for large-scale genomics workloads.
September 2025
Activity
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Quality Metrics
Correctness100.0%
Maintainability93.4%
Architecture100.0%
Performance80.0%
AI Usage60.0%
Skills & Technologies
Programming Languages
PythonShellYAML
Technical Skills
BioinformaticsCSVData ConversionPython ScriptingShell ScriptingSnakemakeVCF ProcessingVariant AnnotationWorkflow ManagementYAMLYAML Configurationbioinformaticsdata processingworkflow managementwrapper development
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