nf-core/modules
May 2025 – May 2026
4 Months active
Languages Used
GroovyYAMLnfyamlDockerfileNextflow
Technical Skills
BioinformaticsImage ProcessingNextflowBioinformatics PipelinesModule DevelopmentData Processing
Carolin Schwitalla
PROFILE
Carolin Schwitalla
Over four months, contributed to the nf-core/modules repository by developing five new features focused on bioinformatics pipelines and data interoperability. Built modules for converting diverse image formats to OME-Zarr and OME-TIFF, enabling standardized workflows for light-sheet microscopy data. Leveraged Nextflow, Docker, and Groovy to containerize tools, automate testing, and streamline environment configuration. Enhanced data processing by introducing a MATLAB mat2json converter and improved usability of the macsima2mc tool through naming and workflow refinements. Emphasized reproducibility and CI hygiene by updating documentation, metadata, and test automation, supporting reliable integration and deployment of modular bioinformatics workflows across research environments.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
5Total
Bugs
0
Commits
5
Features
5
Lines of code
1,514
Activity Months4
Your Network
202 peopleSame Organization
@uni-tuebingen.de22
Work History
May 2026
1 Commits • 1 Features
May 1, 2026May 2026: Focused on improving the Macsima2mc tool usability and aligning its naming conventions within nf-core/modules. Delivered a targeted feature enhancement that refines the macsima2mc tool and fixes naming for clearer usage and easier downstream integration. The change was implemented via a commit updating the macsima2mc tool and correcting naming, supporting better user experience and maintenance.
1 Commits • 1 Features
May 1, 2026May 2026: Focused on improving the Macsima2mc tool usability and aligning its naming conventions within nf-core/modules. Delivered a targeted feature enhancement that refines the macsima2mc tool and fixes naming for clearer usage and easier downstream integration. The change was implemented via a commit updating the macsima2mc tool and correcting naming, supporting better user experience and maintenance.
May 2026
March 2026
2 Commits • 2 Features
Mar 1, 2026March 2026 monthly summary for nf-core/modules focusing on delivered features, bug fixes, and business impact. Demonstrated strong data interoperability, reproducibility, and CI hygiene through containerized deployments and module enhancements.
March 2026
2 Commits • 2 Features
Mar 1, 2026March 2026 monthly summary for nf-core/modules focusing on delivered features, bug fixes, and business impact. Demonstrated strong data interoperability, reproducibility, and CI hygiene through containerized deployments and module enhancements.
June 2025
1 Commits • 1 Features
Jun 1, 2025June 2025: Delivered a new Zarr-to-OME-TIFF conversion module with pyramid generation for nf-core/modules. Implemented environment setup, processing workflow, and testing configuration, enabling reliable conversion of Zarr-formatted image tiles into OME-TIFF pyramids and enabling downstream analysis and visualization via Raw2ometiff integration. This work strengthens repository capabilities for scalable imaging pipelines and interoperability with common bioimaging formats.
1 Commits • 1 Features
Jun 1, 2025June 2025: Delivered a new Zarr-to-OME-TIFF conversion module with pyramid generation for nf-core/modules. Implemented environment setup, processing workflow, and testing configuration, enabling reliable conversion of Zarr-formatted image tiles into OME-TIFF pyramids and enabling downstream analysis and visualization via Raw2ometiff integration. This work strengthens repository capabilities for scalable imaging pipelines and interoperability with common bioimaging formats.
June 2025
May 2025
1 Commits • 1 Features
May 1, 2025Month: May 2025 — nf-core/modules delivered a new capability that enhances data interoperability and pipeline modularity by introducing the Bioformats2Raw module for OME-Zarr conversion. The feature focuses on converting diverse image formats into the OME-Zarr structure, including environment configuration, process definition, and metadata to support OME-NGFF compatibility. The work is in the nf-core/modules repository and tied to a single commit that implements the feature.
May 2025
1 Commits • 1 Features
May 1, 2025Month: May 2025 — nf-core/modules delivered a new capability that enhances data interoperability and pipeline modularity by introducing the Bioformats2Raw module for OME-Zarr conversion. The feature focuses on converting diverse image formats into the OME-Zarr structure, including environment configuration, process definition, and metadata to support OME-NGFF compatibility. The work is in the nf-core/modules repository and tied to a single commit that implements the feature.
Activity
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Quality Metrics
Correctness96.0%
Maintainability88.0%
Architecture96.0%
Performance80.0%
AI Usage32.0%
Skills & Technologies
Programming Languages
DockerfileGroovyNextflowYAMLnfyaml
Technical Skills
BioinformaticsBioinformatics PipelinesData ProcessingDockerImage ProcessingModule DevelopmentNextflowbioinformaticscontainerizationlight-sheet microscopyworkflow development
Repositories Contributed To
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