nf-core/modules
Nov 2024 – Sep 2025
4 Months active
Languages Used
BashGroovyNfYAMLShell
Technical Skills
BioinformaticsContainerizationGenomicsNextflowNextflow ScriptingPipeline Development
Daniel Schmitz
PROFILE
Daniel Schmitz
Daniel Schmitz developed and enhanced bioinformatics modules in the nf-core/modules repository, focusing on tandem repeat genotyping, methylation data integration, and structural variant analysis. He built modular workflows for TRGT and STRdust, enabling robust genotyping of long-read sequencing data, and delivered a BedMethyl to BigWig converter to streamline methylation analysis. Daniel applied containerization and environment management to ensure reproducibility and reliable CI/CD deployment. Using Nextflow, Bash, and YAML, he implemented comprehensive test coverage, standardized metadata, and improved parameter validation. His work addressed both feature development and critical bug fixes, resulting in more flexible, maintainable, and reproducible genomics pipelines.
Overall Statistics
Feature vs Bugs
86%Features
Repository Contributions
8Total
Bugs
1
Commits
8
Features
6
Lines of code
2,288
Activity Months4
Your Network
112 people
Work History
September 2025
2 Commits • 2 Features
Sep 1, 2025September 2025 performance summary for nf-core/modules focused on delivering a methylation data integration workflow and enhancing structural variant analysis with robust containerized deployments and dependency updates.
2 Commits • 2 Features
Sep 1, 2025September 2025 performance summary for nf-core/modules focused on delivering a methylation data integration workflow and enhancing structural variant analysis with robust containerized deployments and dependency updates.
September 2025
April 2025
1 Commits
Apr 1, 2025April 2025 – nf-core/modules: Delivered a critical bug fix to FastQC memory handling, enforcing integer input to prevent precision issues and improve reliability across pipelines. Linked to commit b1966f36ec9de31927b2603d8f499960b2a4c294 (#8180).
April 2025
1 Commits
Apr 1, 2025April 2025 – nf-core/modules: Delivered a critical bug fix to FastQC memory handling, enforcing integer input to prevent precision issues and improve reliability across pipelines. Linked to commit b1966f36ec9de31927b2603d8f499960b2a4c294 (#8180).
March 2025
1 Commits • 1 Features
Mar 1, 2025March 2025 monthly summary for nf-core/modules focusing on delivered capabilities, bug fixes, and overall impact. The primary milestone was the delivery of a new STRdust tandem repeat genotyper module for long reads, expanding the repository’s genomics tooling to support long-read repeat genotyping workflows. The change set includes environment setup, core processing logic, metadata definitions, and robust input/output specifications with region handling support. Comprehensive test coverage ensures validation across parameter variations and region specifications. The work aligns with nf-core modular standards, enabling reliable integration into existing pipelines and facilitating broader adoption in STR genotyping trials.
1 Commits • 1 Features
Mar 1, 2025March 2025 monthly summary for nf-core/modules focusing on delivered capabilities, bug fixes, and overall impact. The primary milestone was the delivery of a new STRdust tandem repeat genotyper module for long reads, expanding the repository’s genomics tooling to support long-read repeat genotyping workflows. The change set includes environment setup, core processing logic, metadata definitions, and robust input/output specifications with region handling support. Comprehensive test coverage ensures validation across parameter variations and region specifications. The work aligns with nf-core modular standards, enabling reliable integration into existing pipelines and facilitating broader adoption in STR genotyping trials.
March 2025
November 2024
4 Commits • 3 Features
Nov 1, 2024Month 2024-11 focused on delivering end-to-end TRGT support in nf-core/modules, enhancing tandem repeat analysis for PacBio HiFi data. Key features include a Genotype module, a dedicated TRGT plotting module, and an enhanced TRGT merge module, each with configuration, main workflow, metadata handling, and tests. Expanded test coverage, including configurable output extensions for stub tests, improves reliability and downstream compatibility. The work standardizes metadata, strengthens reproducibility, and increases pipeline flexibility for researchers analyzing tandem repeats. Technologies and skills demonstrated include: modular nf-core Snakemake-based workflow design, environment/config management, VCF handling and merging, multi-format plotting outputs (PNG/PDF/SVG), and test-driven development with comprehensive unit/integration tests.
November 2024
4 Commits • 3 Features
Nov 1, 2024Month 2024-11 focused on delivering end-to-end TRGT support in nf-core/modules, enhancing tandem repeat analysis for PacBio HiFi data. Key features include a Genotype module, a dedicated TRGT plotting module, and an enhanced TRGT merge module, each with configuration, main workflow, metadata handling, and tests. Expanded test coverage, including configurable output extensions for stub tests, improves reliability and downstream compatibility. The work standardizes metadata, strengthens reproducibility, and increases pipeline flexibility for researchers analyzing tandem repeats. Technologies and skills demonstrated include: modular nf-core Snakemake-based workflow design, environment/config management, VCF handling and merging, multi-format plotting outputs (PNG/PDF/SVG), and test-driven development with comprehensive unit/integration tests.
Activity
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Quality Metrics
Correctness95.0%
Maintainability95.0%
Architecture95.0%
Performance80.0%
AI Usage20.0%
Skills & Technologies
Programming Languages
BashGroovyNfShellYAML
Technical Skills
BioinformaticsBioinformatics PipelinesContainerizationDevOpsGenomicsNextflowNextflow ScriptingPipeline DevelopmentSoftware Engineering
Repositories Contributed To
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