nf-core/modules
Jan 2025 – Apr 2026
7 Months active
Languages Used
GroovyShellnfBashNextflowNfNixYAML
Technical Skills
NextflowShell ScriptingSoftware DevelopmentBioinformaticsWorkflow ManagementAmplicon Sequencing
Sam W
PROFILE
Sam W
Contributed to the nf-core/modules repository by developing and refining bioinformatics workflow modules, focusing on robust input handling, reproducible outputs, and test-driven development. Delivered features such as the Artic AlignTrim module for amplicon sequencing and enhanced decompression workflows, using Nextflow, Shell scripting, and YAML for workflow orchestration and configuration. Addressed edge cases in modules like find/unpigz and RepeatMasker, improving reliability for gzipped and mixed input types. Upgraded dependencies and maintained test snapshots to ensure compatibility and reproducibility. Emphasized modular design, dynamic resource estimation, and clear error handling, resulting in more maintainable, scalable, and user-friendly bioinformatics pipelines.
Overall Statistics
Feature vs Bugs
67%Features
Repository Contributions
10Total
Bugs
3
Commits
10
Features
6
Lines of code
1,352
Activity Months7
Work History
April 2026
1 Commits • 1 Features
Apr 1, 2026April 2026: Completed a key feature upgrade in nf-core/modules by upgrading align_trim from 1.0.2 to 1.1.0. The environment.yml was updated and test snapshots adjusted to reflect the new behavior, preserving pipeline compatibility and reproducibility across environments. No major bugs were introduced; the changes included necessary test maintenance to align with the library upgrade. This work demonstrates strong dependency management, version control discipline, and test snapshot maintenance, delivering business value through more stable, predictable workflows.
1 Commits • 1 Features
Apr 1, 2026April 2026: Completed a key feature upgrade in nf-core/modules by upgrading align_trim from 1.0.2 to 1.1.0. The environment.yml was updated and test snapshots adjusted to reflect the new behavior, preserving pipeline compatibility and reproducibility across environments. No major bugs were introduced; the changes included necessary test maintenance to align with the library upgrade. This work demonstrates strong dependency management, version control discipline, and test snapshot maintenance, delivering business value through more stable, predictable workflows.
April 2026
October 2025
1 Commits • 1 Features
Oct 1, 2025October 2025: Delivered a key feature in the nf-core/modules SAMTOOLS_COVERAGE module that makes FASTA reference input and its index optional, while enforcing that if a CRAM input is used, both FASTA reference and its index must be provided. This enables processing without a reference FASTA in non-CRAM scenarios and preserves correct CRAM usage, improving reliability and user experience.
October 2025
1 Commits • 1 Features
Oct 1, 2025October 2025: Delivered a key feature in the nf-core/modules SAMTOOLS_COVERAGE module that makes FASTA reference input and its index optional, while enforcing that if a CRAM input is used, both FASTA reference and its index must be provided. This enables processing without a reference FASTA in non-CRAM scenarios and preserves correct CRAM usage, improving reliability and user experience.
September 2025
1 Commits • 1 Features
Sep 1, 2025Month: 2025-09 — nf-core/modules: Focused feature delivery and quality improvements around BWAMEM2_INDEX, with an emphasis on accurate resource estimation and testability.
1 Commits • 1 Features
Sep 1, 2025Month: 2025-09 — nf-core/modules: Focused feature delivery and quality improvements around BWAMEM2_INDEX, with an emphasis on accurate resource estimation and testability.
September 2025
August 2025
2 Commits • 1 Features
Aug 1, 2025August 2025: Delivered the initial Artic AlignTrim module for nf-core/modules, enabling soft clipping of primer sites from BAM/SAM files using align_trim and providing reports on primer trimming and amplicon depth. The release is tracked by commits referencing Add artic/aligntrim module (#8943) and Bump artic_aligntrim version (#8969), reinforcing reproducibility and standardization across nf-core pipelines. No major bugs reported this month. Impact: accelerates deployment of amplicon sequencing workflows, improves data quality through standardized primer clipping and depth reporting. Technologies/skills demonstrated: modular design, integration with alignment-based tools, release management, and git traceability.
August 2025
2 Commits • 1 Features
Aug 1, 2025August 2025: Delivered the initial Artic AlignTrim module for nf-core/modules, enabling soft clipping of primer sites from BAM/SAM files using align_trim and providing reports on primer trimming and amplicon depth. The release is tracked by commits referencing Add artic/aligntrim module (#8943) and Bump artic_aligntrim version (#8969), reinforcing reproducibility and standardization across nf-core pipelines. No major bugs reported this month. Impact: accelerates deployment of amplicon sequencing workflows, improves data quality through standardized primer clipping and depth reporting. Technologies/skills demonstrated: modular design, integration with alignment-based tools, release management, and git traceability.
June 2025
2 Commits
Jun 1, 2025June 2025 monthly summary for nf-core/modules: Delivered targeted bug fixes to improve reliability and consistency in input handling and output generation, with test coverage and configuration updates to support reproducible pipelines. The changes reduce downstream pipeline failures and improve automation, especially when using gzipped FASTA inputs.
2 Commits
Jun 1, 2025June 2025 monthly summary for nf-core/modules: Delivered targeted bug fixes to improve reliability and consistency in input handling and output generation, with test coverage and configuration updates to support reproducible pipelines. The changes reduce downstream pipeline failures and improve automation, especially when using gzipped FASTA inputs.
June 2025
February 2025
1 Commits • 1 Features
Feb 1, 2025February 2025 – nf-core/modules: Key feature delivered was a refactor of the find/unpigz workflow to output decompressed files into a dedicated 'ungzipped' directory, accompanied by enhanced tests. Major quality work included adding test assertions to verify the existence and count of decompressed files, boosting test coverage and robustness (commit 9b74dcad06abf4905524411c72efada0e5e189d9; PR #7425). Overall impact: more reliable decompression behavior, clearer module semantics, and reduced risk in CI and downstream pipelines. Technologies/skills demonstrated: Nextflow module development, refactoring, test-driven development, and test automation; demonstrated ability to tighten test suites and improve maintainability across the nf-core/modules repository.
February 2025
1 Commits • 1 Features
Feb 1, 2025February 2025 – nf-core/modules: Key feature delivered was a refactor of the find/unpigz workflow to output decompressed files into a dedicated 'ungzipped' directory, accompanied by enhanced tests. Major quality work included adding test assertions to verify the existence and count of decompressed files, boosting test coverage and robustness (commit 9b74dcad06abf4905524411c72efada0e5e189d9; PR #7425). Overall impact: more reliable decompression behavior, clearer module semantics, and reduced risk in CI and downstream pipelines. Technologies/skills demonstrated: Nextflow module development, refactoring, test-driven development, and test automation; demonstrated ability to tighten test suites and improve maintainability across the nf-core/modules repository.
January 2025
2 Commits • 1 Features
Jan 1, 2025January 2025 monthly summary for nf-core/modules: Delivered reliability enhancements and UX improvements to the find/unpigz module. Fixed a crash when processing a single input file by adjusting input arity and added tests to ensure solitary inputs are handled robustly. Implemented naming consistency for decompressed outputs by removing the extra prefix, aligning filenames with the original gzipped input and updating snapshot tests. The changes improve downstream predictability, reduce edge-case failures, and demonstrate strong testing and quality assurance practices.
2 Commits • 1 Features
Jan 1, 2025January 2025 monthly summary for nf-core/modules: Delivered reliability enhancements and UX improvements to the find/unpigz module. Fixed a crash when processing a single input file by adjusting input arity and added tests to ensure solitary inputs are handled robustly. Implemented naming consistency for decompressed outputs by removing the extra prefix, aligning filenames with the original gzipped input and updating snapshot tests. The changes improve downstream predictability, reduce edge-case failures, and demonstrate strong testing and quality assurance practices.
January 2025
Activity
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Quality Metrics
Correctness91.0%
Maintainability90.0%
Architecture88.0%
Performance84.0%
AI Usage20.0%
Skills & Technologies
Programming Languages
BashGroovyNextflowNfNixShellYAMLnf
Technical Skills
Amplicon SequencingBioinformaticsContinuous IntegrationDependency ManagementDevOpsGenomicsNextflowShell ScriptingSoftware DevelopmentSoftware EngineeringWorkflow Managementbioinformaticsdata processing
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