snakemake/snakemake-wrappers
Nov 2024 – Jul 2025
6 Months active
Languages Used
PythonRYAMLPerlShellVCF
Technical Skills
BioinformaticsCI/CDCondaDocumentationShell ScriptingSnakemake
tdayris
PROFILE
Tdayris
Over six months, contributed a series of production-ready workflow wrappers to the snakemake/snakemake-wrappers repository, focusing on reproducibility and automation in bioinformatics pipelines. Developed and enhanced wrappers for tools such as MTNucRatioCalculator, Sex.detERRmine, NGS-bits, Varscan2, SnpEff, bwameth, DESeq2, and AGAT, integrating Python, R, and Shell scripting. Implemented robust environment management with Conda, comprehensive test coverage, and CI/CD readiness to ensure reliability across diverse computing environments. Addressed workflow portability and debugging by improving logging, configuration, and error handling. The work streamlined NGS data analysis, variant annotation, and workflow management for genomics teams using Snakemake.
Overall Statistics
Feature vs Bugs
83%Features
Repository Contributions
15Total
Bugs
2
Commits
15
Features
10
Lines of code
64,299
Activity Months6
Your Network
128 peopleWork History
July 2025
1 Commits • 1 Features
Jul 1, 2025July 2025 monthly summary: Delivered AGAT tool wrapper integration for Snakemake in the snakemake-wrappers repository, enabling standardized execution of AGAT subcommands within Snakemake workflows. Implemented environment specifications, metadata, and a versatile wrapper, plus automated test workflows and test data to validate integration.
1 Commits • 1 Features
Jul 1, 2025July 2025 monthly summary: Delivered AGAT tool wrapper integration for Snakemake in the snakemake-wrappers repository, enabling standardized execution of AGAT subcommands within Snakemake workflows. Implemented environment specifications, metadata, and a versatile wrapper, plus automated test workflows and test data to validate integration.
July 2025
June 2025
4 Commits • 1 Features
Jun 1, 2025Concise monthly performance summary for 2025-06 focused on the snakemake-wrappers repository. Delivered feature enhancements and bug fixes that improve reliability, portability, and observability of workflow wrappers. Emphasis on business value: robust data access, consistent behavior across environments, and easier debugging for large-scale pipelines.
June 2025
4 Commits • 1 Features
Jun 1, 2025Concise monthly performance summary for 2025-06 focused on the snakemake-wrappers repository. Delivered feature enhancements and bug fixes that improve reliability, portability, and observability of workflow wrappers. Emphasis on business value: robust data access, consistent behavior across environments, and easier debugging for large-scale pipelines.
May 2025
2 Commits • 2 Features
May 1, 2025May 2025 performance summary for snakemake/snakemake-wrappers: Delivered two production-ready wrappers that boost reproducibility and accuracy of sequencing workflows. The BWAMETH BS-Seq alignment wrapper was added with test coverage across sorting configurations and defined conda environments to ensure consistent runs. The DESeq2 Wald analysis wrapper was upgraded to support apeglm shrinkage, with improved contrast naming and result labeling, plus expanded tests covering apeglm, ashr, and normal shrinkage, and fixes to parameter naming and error handling. These workstreams reduce pipeline errors, improve reliability across teams, and streamline deployment in CI environments.
2 Commits • 2 Features
May 1, 2025May 2025 performance summary for snakemake/snakemake-wrappers: Delivered two production-ready wrappers that boost reproducibility and accuracy of sequencing workflows. The BWAMETH BS-Seq alignment wrapper was added with test coverage across sorting configurations and defined conda environments to ensure consistent runs. The DESeq2 Wald analysis wrapper was upgraded to support apeglm shrinkage, with improved contrast naming and result labeling, plus expanded tests covering apeglm, ashr, and normal shrinkage, and fixes to parameter naming and error handling. These workstreams reduce pipeline errors, improve reliability across teams, and streamline deployment in CI environments.
May 2025
February 2025
1 Commits • 1 Features
Feb 1, 2025February 2025: Delivered an end-to-end somatic variant annotation workflow integration within the Snakemake wrappers repository, introducing a Varscan2-SnpEff meta-wrapper. This work adds cohesive cross-tool orchestration (Samtools, Varscan2, SnpEff) into a single, reproducible pipeline, along with new configuration files, a test Snakefile, and a dedicated test function to validate the integrated workflow. The changes enhance automation, reliability, and reproducibility for somatic variant annotation workflows in downstream analyses.
February 2025
1 Commits • 1 Features
Feb 1, 2025February 2025: Delivered an end-to-end somatic variant annotation workflow integration within the Snakemake wrappers repository, introducing a Varscan2-SnpEff meta-wrapper. This work adds cohesive cross-tool orchestration (Samtools, Varscan2, SnpEff) into a single, reproducible pipeline, along with new configuration files, a test Snakefile, and a dedicated test function to validate the integrated workflow. The changes enhance automation, reliability, and reproducibility for somatic variant annotation workflows in downstream analyses.
December 2024
4 Commits • 2 Features
Dec 1, 2024December 2024 monthly summary for snakemake/snakemake-wrappers: - Key features delivered: Implemented end-to-end wrappers for NGS-bits SampleAncestry and SampleSimilarity to enable comprehensive ancestry estimation and sample similarity analysis directly in Snakemake workflows, including environment setup, metadata handling, and tests. - Major features added: Delivered NGSCheckMate wrapper with multi-input support (BAM/VCF/FASTQ) and SNP pattern generation, enhancing capability to identify related samples and analyze SNP patterns in sequencing data. - Focused on automation and reproducibility: Added environment provisioning, metadata schemas, and robust tests for wrappers to ensure reliable, repeatable analyses across projects. - Impact: Accelerates pipeline integration for sequencing analyses, improves reproducibility, and broadens the platform’s NGS workflow capabilities with end-to-end solutions. - Technologies/skills demonstrated: Snakemake wrappers design, NGS-bits integration, multi-input wrapper development, SNP pattern logic, environment and test automation; commits consolidated across two feature sets.
4 Commits • 2 Features
Dec 1, 2024December 2024 monthly summary for snakemake/snakemake-wrappers: - Key features delivered: Implemented end-to-end wrappers for NGS-bits SampleAncestry and SampleSimilarity to enable comprehensive ancestry estimation and sample similarity analysis directly in Snakemake workflows, including environment setup, metadata handling, and tests. - Major features added: Delivered NGSCheckMate wrapper with multi-input support (BAM/VCF/FASTQ) and SNP pattern generation, enhancing capability to identify related samples and analyze SNP patterns in sequencing data. - Focused on automation and reproducibility: Added environment provisioning, metadata schemas, and robust tests for wrappers to ensure reliable, repeatable analyses across projects. - Impact: Accelerates pipeline integration for sequencing analyses, improves reproducibility, and broadens the platform’s NGS workflow capabilities with end-to-end solutions. - Technologies/skills demonstrated: Snakemake wrappers design, NGS-bits integration, multi-input wrapper development, SNP pattern logic, environment and test automation; commits consolidated across two feature sets.
December 2024
November 2024
3 Commits • 3 Features
Nov 1, 2024November 2024 performance summary focused on enabling robust Snakemake integration for MTNucRatioCalculator and Sex.detERRmine via wrappers, plus contributor documentation improvements in snakemake/snakemake-wrappers. Deliverables emphasize reproducibility, CI readiness, and streamlined pipeline integration with end-to-end test coverage and multi-format outputs.
November 2024
3 Commits • 3 Features
Nov 1, 2024November 2024 performance summary focused on enabling robust Snakemake integration for MTNucRatioCalculator and Sex.detERRmine via wrappers, plus contributor documentation improvements in snakemake/snakemake-wrappers. Deliverables emphasize reproducibility, CI readiness, and streamlined pipeline integration with end-to-end test coverage and multi-format outputs.
Activity
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Quality Metrics
Correctness97.4%
Maintainability96.0%
Architecture96.6%
Performance82.0%
AI Usage53.4%
Skills & Technologies
Programming Languages
PerlPythonRShellVCFYAML
Technical Skills
BioinformaticsCI/CDCondaConda Environment ManagementConda EnvironmentsData AnalysisDocumentationGenomicsNGS Data AnalysisPython DevelopmentPython ScriptingR ProgrammingShell ScriptingSnakemakeTechnical Writing
Repositories Contributed To
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