nf-core/modules
Dec 2024 – May 2026
11 Months active
Languages Used
NfYAMLGroovynfShellAwkNfcoreNextflow
Technical Skills
Bioinformatics PipelinesNextflowSoftware UpdatesContainerizationdata processingpipeline development
Charles Plessy
PROFILE
Charles Plessy
Over eleven months, this developer enhanced the nf-core/modules repository by building and refining bioinformatics pipelines focused on data processing, compression, and workflow reliability. They implemented features such as parallel MAF conversion, taxonomy-aware database creation, and unified output handling for DotPlot and MAFConvert modules, using Nextflow, Shell, and AWK scripting. Their work addressed compatibility and reproducibility by upgrading tool versions, improving CRAM/BAM support, and optimizing resource allocation. They also fixed bugs affecting alignment statistics and test reliability, introduced robust FASTA processing subworkflows, and strengthened CI through comprehensive testing, contributing to more maintainable, efficient, and reproducible bioinformatics workflows.
Overall Statistics
Feature vs Bugs
72%Features
Repository Contributions
23Total
Bugs
5
Commits
23
Features
13
Lines of code
3,855
Activity Months11
Work History
May 2026
2 Commits • 1 Features
May 1, 2026In May 2026, nf-core/modules delivered reliability improvements and foundational workflow enhancements. Key work included lint error fixes tied to LAST module updates, enhanced reference genome handling for robust processing, and the introduction of a new FASTA processing subworkflow to support BGZF compression, indexing, and sequence dictionaries for improved CRAM creation. Updated dependencies, snapshots, and test coverage to ensure compatibility with CRAM 3.1 and current tooling.
2 Commits • 1 Features
May 1, 2026In May 2026, nf-core/modules delivered reliability improvements and foundational workflow enhancements. Key work included lint error fixes tied to LAST module updates, enhanced reference genome handling for robust processing, and the introduction of a new FASTA processing subworkflow to support BGZF compression, indexing, and sequence dictionaries for improved CRAM creation. Updated dependencies, snapshots, and test coverage to ensure compatibility with CRAM 3.1 and current tooling.
May 2026
March 2026
1 Commits • 1 Features
Mar 1, 2026Month: 2026-03 — nf-core/modules delivered taxonomy-aware database creation improvements by adding a taxonomic ID mapping input channel to blast/makeblastedb, enabling taxID mapping during database creation. Updated tests to cover the new input channel and validate handling of custom sequence IDs with tax IDs. Also fixed input channel configurations in tests for blast/makeblastdb to improve test reliability. This work enhances taxonomy accuracy in downstream analyses, reduces configuration errors, and strengthens reproducibility. Demonstrated nf-core modular development, Python module work, test-driven development, and collaborative Git workflows (co-authored by Lucia Zifcakova).
March 2026
1 Commits • 1 Features
Mar 1, 2026Month: 2026-03 — nf-core/modules delivered taxonomy-aware database creation improvements by adding a taxonomic ID mapping input channel to blast/makeblastedb, enabling taxID mapping during database creation. Updated tests to cover the new input channel and validate handling of custom sequence IDs with tax IDs. Also fixed input channel configurations in tests for blast/makeblastdb to improve test reliability. This work enhances taxonomy accuracy in downstream analyses, reduces configuration errors, and strengthens reproducibility. Demonstrated nf-core modular development, Python module work, test-driven development, and collaborative Git workflows (co-authored by Lucia Zifcakova).
January 2026
1 Commits • 1 Features
Jan 1, 2026Executive monthly summary for 2026-01 focusing on business value and technical achievements in nf-core/modules. Delivered a key feature that unifies output handling by merging multiple optional output channels into a single output channel, enabling GIF/PNG outputs for DotPlot and supporting various alignment formats for MAFConvert. This reduction in surface area simplifies usage, decreases maintenance overhead, and accelerates downstream workflows. The update aligns with nf-core guidelines and paves the way for easier future enhancements and broader format support. Impact highlights include improved pipeline efficiency, easier downstream data consumption, and a clearer path for future feature additions. The work demonstrates solid version-control practices, refactoring for maintainability, and cross-format compatibility.
1 Commits • 1 Features
Jan 1, 2026Executive monthly summary for 2026-01 focusing on business value and technical achievements in nf-core/modules. Delivered a key feature that unifies output handling by merging multiple optional output channels into a single output channel, enabling GIF/PNG outputs for DotPlot and supporting various alignment formats for MAFConvert. This reduction in surface area simplifies usage, decreases maintenance overhead, and accelerates downstream workflows. The update aligns with nf-core guidelines and paves the way for easier future enhancements and broader format support. Impact highlights include improved pipeline efficiency, easier downstream data consumption, and a clearer path for future feature additions. The work demonstrates solid version-control practices, refactoring for maintainability, and cross-format compatibility.
January 2026
October 2025
1 Commits
Oct 1, 20252025-10 nf-core/modules delivered a critical bug fix that improves the accuracy of alignment statistics by correcting the substitution percent identity calculation. The update selects the second-to-last occurrence to avoid rounding errors in integer matrices, with snapshot tests and versioning updated to reflect the change. This work enhances data reliability for downstream analyses and strengthens overall test coverage and traceability.
October 2025
1 Commits
Oct 1, 20252025-10 nf-core/modules delivered a critical bug fix that improves the accuracy of alignment statistics by correcting the substitution percent identity calculation. The update selects the second-to-last occurrence to avoid rounding errors in integer matrices, with snapshot tests and versioning updated to reflect the change. This work enhances data reliability for downstream analyses and strengthens overall test coverage and traceability.
September 2025
2 Commits • 1 Features
Sep 1, 2025Month: 2025-09 — nf-core/modules: Last module enhancements for data output and performance. Delivered genome statistics extension for MultiQC, injected sequence length into GFF files, enforced CRAM version 3.0 for compatibility with current samtools, and tuned last/split resource allocation to improve parallelism. Fixed shell escaping issues in .command.sh to prevent stray tabs. Aligned nf-test stability by avoiding CRAM 3.1 paths that could cause crashes, ensuring continued compatibility with the broader toolchain. These changes improve data quality, reliability, and throughput for large-scale genome analyses while maintaining compatibility with widely used bioinformatics tools.
2 Commits • 1 Features
Sep 1, 2025Month: 2025-09 — nf-core/modules: Last module enhancements for data output and performance. Delivered genome statistics extension for MultiQC, injected sequence length into GFF files, enforced CRAM version 3.0 for compatibility with current samtools, and tuned last/split resource allocation to improve parallelism. Fixed shell escaping issues in .command.sh to prevent stray tabs. Aligned nf-test stability by avoiding CRAM 3.1 paths that could cause crashes, ensuring continued compatibility with the broader toolchain. These changes improve data quality, reliability, and throughput for large-scale genome analyses while maintaining compatibility with widely used bioinformatics tools.
September 2025
July 2025
1 Commits
Jul 1, 20252025-07 monthly summary for nf-core/modules: Addressed CRAM conversion stability and test reliability by removing FASTA export during CRAM conversion to eliminate race conditions; simplified test data access by removing FASTA export, improving reliability and CI consistency. Commit c1de1f68429a3e9d3bf862276ab4bb41fe606051 implements the change.
July 2025
1 Commits
Jul 1, 20252025-07 monthly summary for nf-core/modules: Addressed CRAM conversion stability and test reliability by removing FASTA export during CRAM conversion to eliminate race conditions; simplified test data access by removing FASTA export, improving reliability and CI consistency. Commit c1de1f68429a3e9d3bf862276ab4bb41fe606051 implements the change.
May 2025
7 Commits • 4 Features
May 1, 2025May 2025 monthly summary for nf-core/modules focusing on delivering robust data processing capabilities, enhanced provenance, and improved QC metrics. Implementations span BGZF compression for FASTA, enhanced MAF/mafconvert workflow, improved LAST alignment metrics, and SAMtools merge with gzi index support. These changes collectively improve data reliability, performance, and downstream reporting in end-to-end pipelines.
7 Commits • 4 Features
May 1, 2025May 2025 monthly summary for nf-core/modules focusing on delivering robust data processing capabilities, enhanced provenance, and improved QC metrics. Implementations span BGZF compression for FASTA, enhanced MAF/mafconvert workflow, improved LAST alignment metrics, and SAMtools merge with gzi index support. These changes collectively improve data reliability, performance, and downstream reporting in end-to-end pipelines.
May 2025
March 2025
2 Commits • 1 Features
Mar 1, 2025March 2025 monthly summary for nf-core/modules focusing on delivering parallel data processing capabilities, improving output integrity, and enhancing reproducibility across the pipeline. The work this month centered on enabling parallel MAF conversion within nf-core/modules, hardening output handling, and upgrading core modules to stable versions to ensure compatibility across downstream analyses and CI.
March 2025
2 Commits • 1 Features
Mar 1, 2025March 2025 monthly summary for nf-core/modules focusing on delivering parallel data processing capabilities, improving output integrity, and enhancing reproducibility across the pipeline. The work this month centered on enabling parallel MAF conversion within nf-core/modules, hardening output handling, and upgrading core modules to stable versions to ensure compatibility across downstream analyses and CI.
February 2025
3 Commits • 2 Features
Feb 1, 2025February 2025: Implemented CRAM/BAM support in last/mafconvert, and enhanced dotplot with TrueType font rendering for sequence names, optional alignment input filtering, plus bug fixes and CI/test updates. These changes broaden data format compatibility, improve visualization reliability, and optimize handling of large inputs.
3 Commits • 2 Features
Feb 1, 2025February 2025: Implemented CRAM/BAM support in last/mafconvert, and enhanced dotplot with TrueType font rendering for sequence names, optional alignment input filtering, plus bug fixes and CI/test updates. These changes broaden data format compatibility, improve visualization reliability, and optimize handling of large inputs.
February 2025
January 2025
2 Commits • 1 Features
Jan 1, 2025January 2025 monthly summary for nf-core/modules: Delivered a major tool upgrade and QA fixes across the module suite, enhancing reproducibility, deployment reliability, and alignment with current best practices. Key outcomes include upgrading the LAST tool to version 1608 across modules (dotplot, lastal, lastdb, mafconvert, mafswap, postmask, split, train) with container and environment updates, migrating the container registry to Seqera's community registry, and refreshing test snapshots to reflect new versions and container URIs. Also fixed a bug in the versions.yml generation caused by escape sequences in the shell script, restoring correct indentation and pipeline functionality. These changes improve cross-module compatibility, CI reliability, and end-to-end reproducibility for LAST-dependent workflows.
January 2025
2 Commits • 1 Features
Jan 1, 2025January 2025 monthly summary for nf-core/modules: Delivered a major tool upgrade and QA fixes across the module suite, enhancing reproducibility, deployment reliability, and alignment with current best practices. Key outcomes include upgrading the LAST tool to version 1608 across modules (dotplot, lastal, lastdb, mafconvert, mafswap, postmask, split, train) with container and environment updates, migrating the container registry to Seqera's community registry, and refreshing test snapshots to reflect new versions and container URIs. Also fixed a bug in the versions.yml generation caused by escape sequences in the shell script, restoring correct indentation and pipeline functionality. These changes improve cross-module compatibility, CI reliability, and end-to-end reproducibility for LAST-dependent workflows.
December 2024
1 Commits • 1 Features
Dec 1, 2024December 2024: nf-core/modules delivered a critical enhancement by upgrading the LAST aligner to v1595 across the module set and fixing output file naming in the last/train module to ensure consistent naming and downstream compatibility. This change reduces downstream errors and improves reproducibility across pipelines. Implemented via commit 3c7402ae39bd7104740bd6e7e60301b94ecb8fe5 and aligns with our focus on reliability and maintainability.
1 Commits • 1 Features
Dec 1, 2024December 2024: nf-core/modules delivered a critical enhancement by upgrading the LAST aligner to v1595 across the module set and fixing output file naming in the last/train module to ensure consistent naming and downstream compatibility. This change reduces downstream errors and improves reproducibility across pipelines. Implemented via commit 3c7402ae39bd7104740bd6e7e60301b94ecb8fe5 and aligns with our focus on reliability and maintainability.
December 2024
Activity
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Quality Metrics
Correctness91.8%
Maintainability88.6%
Architecture87.8%
Performance83.6%
AI Usage24.4%
Skills & Technologies
Programming Languages
AwkGroovyNextflowNfNfcoreShellYAMLnf
Technical Skills
AWK ScriptingBioinformaticsBioinformatics PipelinesCommand Line InterfaceCommand Line ToolsContainerizationData AnalysisData CompressionMAF conversionNextflowSamtoolsScriptingShell ScriptingSoftware EngineeringSoftware Updates
Repositories Contributed To
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