nf-core/modules
Nov 2024 – Feb 2026
6 Months active
Languages Used
BashGroovyNfYAMLShell
Technical Skills
BioinformaticsContainerizationGenomicsNextflowNextflow ScriptingPipeline Development
Daniel Schmitz
PROFILE
Daniel Schmitz
Over six months, contributed to the nf-core/modules repository by developing and enhancing bioinformatics pipeline modules for genomics research. Built end-to-end solutions for tandem repeat genotyping, methylation data integration, and sample processing, leveraging Nextflow, Bash, and YAML to ensure modularity and reproducibility. Delivered features such as TRGT and STRdust modules for long-read analysis, a BedMethyl to BigWig converter, and a SAMtools-based processing workflow, each with robust test coverage and metadata standardization. Addressed pipeline reliability by fixing memory handling in FastQC and improving output validation for Sawfish joint calling, emphasizing containerization, environment management, and adherence to nf-core standards throughout.
Overall Statistics
Feature vs Bugs
89%Features
Repository Contributions
10Total
Bugs
1
Commits
10
Features
8
Lines of code
3,462
Activity Months6
Your Network
188 peopleWork History
February 2026
1 Commits • 1 Features
Feb 1, 2026February 2026 – nf-core/modules: Delivered the maf_bw output channel for Sawfish joint calling to emit MAF BigWig files, with updated metadata, tests, and BigWig ontology integration to ensure correct generation and validation in genomic analyses. Also fixed MAF output in stub and completed missing parts of metadata, moving versions to the topic channel to improve release hygiene. The work enhances downstream interoperability, reproducibility, and data quality for Sawfish analyses.
1 Commits • 1 Features
Feb 1, 2026February 2026 – nf-core/modules: Delivered the maf_bw output channel for Sawfish joint calling to emit MAF BigWig files, with updated metadata, tests, and BigWig ontology integration to ensure correct generation and validation in genomic analyses. Also fixed MAF output in stub and completed missing parts of metadata, moving versions to the topic channel to improve release hygiene. The work enhances downstream interoperability, reproducibility, and data quality for Sawfish analyses.
February 2026
November 2025
1 Commits • 1 Features
Nov 1, 2025Concise monthly summary for 2025-11 focusing on nf-core/modules contributions, business value, and technical achievements. The team delivered a SAMtools-based sample processing module with robust tests and metadata alignment, improving reproducibility and maintainability of module workflows.
November 2025
1 Commits • 1 Features
Nov 1, 2025Concise monthly summary for 2025-11 focusing on nf-core/modules contributions, business value, and technical achievements. The team delivered a SAMtools-based sample processing module with robust tests and metadata alignment, improving reproducibility and maintainability of module workflows.
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
Correctness94.0%
Maintainability92.0%
Architecture94.0%
Performance80.0%
AI Usage22.0%
Skills & Technologies
Programming Languages
BashGroovyNfShellYAML
Technical Skills
BioinformaticsBioinformatics PipelinesContainerizationDevOpsGenomicsNextflowNextflow ScriptingPipeline DevelopmentSoftware Engineeringbioinformaticsdata analysisdata processinggenomics
Repositories Contributed To
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