v0.6.0 - UnleashedSplicingViper: Coming in from behind the curtain

NeoRasp v0.6.0 - UnleashedSplicingViper 🐍

Built behind the curtain, now on stage for everyone to run

This release updates the workflow and testing configuration to improve compatibility with CI environments, updates dependencies, and simplifies test setup. The main changes focus on standardizing environment variables for containerized tests, updating dependency versions, and consolidating test tags and configuration.

CI and Environment Improvements:

• Added WORKSPACE and APPTAINER_HPC environment variables to the CI workflow and ensured necessary cache directories are created before running tests (.github/workflows/ci.yml).

Dependency and Configuration Updates:

• Updated snakemake-minimal dependency to a newer version range.
• Changed pytest command tag from localintegrationtest to integrationtest in pixi.toml to align with updated test tagging.

Test Tag and Config Consolidation:

• Updated all relevant test tags from localintegrationtest to integrationtest and added ci tag for CI compatibility in tests/test_issue/test_fixed_issues.yaml and tests/test_splicing.yaml.
• Refactored test commands to use configuration files instead of inline configs for splice2neo tests, and added new config files with scatter_size parameters.

Test Cleanup and Simplification:

• Removed redundant "local" test variants and streamlined test commands to use the new environment variables and tags in tests/test_splicing.yaml.

Full Changelog: v0.5.0...v0.6.0

v0.5.0 - FeastySplicingViper: Docs in Harmony🐍

NeoRasp v0.5.0 - FeastySplicingViper: Docs in Harmony🐍

The viper got wiser: cleaner docs, cleaner docstrings, smoother splices.”

This release introduces several improvements to documentation, repository configuration, and workflow management for the NeoRasp pipeline. The main changes include a comprehensive update of the README.md, addition of contribution guidelines, improved documentation structure, and updates to CI/CD and configuration files.

What's Changed

Documentation updates:

• Rewrite and reorganization of README.md to clarify installation, usage, input/output, and contribution instructions, and to update links and references for the GitHub repository.
• Addition of CONTRIBUTING.md with clear guidelines for contributing, including documentation and pipeline module development.
• Addition and update of documentation files in documentation/neorasp/docs/, including about.md, faq.md, installation.md, and references.md, with improved instructions, FAQ entries, and updated references.
• Updates to developer guide and cluster documentation to fix links, clarify plugin usage

CI/CD and Workflow Configuration:

• Addition of a path filter to the CI workflow (.github/workflows/ci.yml) to skip pipeline runs for documentation-only changes.
• Removal of the legacy release-please.yaml workflow.

Configuration Updates:

• Addition of a config validation schema which provides default values for test runs, allowing to drop example configs.
• Addition of a usage section to .snakemake-workflow-catalog.yml to clarify supported deployment methods.

Catalog Updates:

• Addition of a usage section to .snakemake-workflow-catalog.yml to clarify supported deployment methods.

v0.4.0 - FeastySplicingViper: No Mamba, No Cry 🐍

NeoRasp v0.4.0 - FeastySplicingViper: “No Mamba, No Cry” 🐍

The viper is now cached, locked, and ready to splice

This release introduces significant improvements to the development workflow, documentation, and CI/CD setup, centering the project around Pixi for environment and task management. It replaces previous Conda/Mamba-based workflows with Pixi, updates and clarifies documentation, and refines several project files for better maintainability and clarity.

Development and CI/CD environment modernization:

• Migrated all CI workflows (.github/workflows/ci.yml, .github/workflows/static.yml) from Conda/Mamba to Pixi for environment management and task execution, simplifying setup and caching dependencies for faster builds.
• Removed the Makefile, eliminating legacy local integration test logic and environment variable checks.

Documentation and developer experience:

• Added a comprehensive developer guide (documentation/tronmake-rna-splicing/docs/developer_guide.md) detailing Pixi usage, available tasks, testing, code styling, and release process.
• Updated the main README.md and documentation for clarity, improved formatting, accurate workflow descriptions, and to reflect the Pixi-based workflow and new features (such as technical replicate support and mouse model notes).
• Added a new FAQ section covering supported splicing events, mouse model support, troubleshooting, and gene exclusion filters.

Other project maintenance:

• Corrected the copyright year in LICENSE.

v0.3.0 - FeastySplicingViper: HydrAI edition 🐍🤖🐍

NeoRasp v0.3.0 - FeastySplicingViper: HydrAI edition 🐍🤖🐍

The viper received some bug fixes and improvements for faster hunting, as well as AmazIng documentation updates.

What's Changed

Changes:

• Snakemake v9.13.7 upgrade
• Enhanced CI/CD pipeline with additional integration tests (CI/CD and local integration tests)
• Snakemake pathvars implementation
• STAR index moved from params to rule input
• STAR output naming updated for inclusion in MultiQC
• Fixed scatter-gather bug when yielding single file
• Fixed BSGenome bug by forcing atomar operation on temporary genome file

Documentation:

• Updated Snakemake version from 8.24.1 → 9.13.7 in README.md, docs/index.md, and environment.ci.yaml
• Documented STAR output files now include sample name prefix (e.g., {sample}_Aligned.sortedByCoord.out.cram)
• Added comprehensive output files list in output.md
• Documented new target rules: only_alignment and only_splice2neo for partial pipeline execution
• Added pathvars section explaining Snakemake pathvars implementation for workflow reuse
• Added testing documentation including Makefile usage and test categories (CI vs local integration tests)

CI/CD Pipeline Fixes:

• Created environment.ci.yaml - a CI-specific environment file without SLURM executor plugin
• Updated .github/workflows/ci.yml to use the new CI environment file for all jobs (syntaxcheck, linting, integration)
• Fixes error where snakemake-executor-plugin-slurm was attempting to find sacct/squeue commands on Ubuntu runners
• Added disk space optimization: Cleanup of unused software (dotnet, Android SDK, GHC, CodeQL tools) before tests to free ~17GB
• Removed Apptainer cache to save disk space (not needed for CI tests)
• Added disk usage monitoring with df -h before/after cleanup and at completion
• Changed integration test tag from integrationtest to ci for CI-specific test execution

Contributors

@johausmann
@Tishwings

v0.2.1 - FeastySplicingViper: Hydra Edition 🐍🐍🐍

NeoRasp v0.2.1 - FeastySplicingViper: Hydra edition 🐍🐍🐍

The viper needed a fix to ignore non-tasty, non-coding regions in the petide annotation.

What's Changed

• Updated gene annotation step to remove junctions in non-CDS transcripts from further processing
• Updated peptide annotation to use process safe BSGenome

Full Changelog: v0.2.0...v0.2.1

v0.2.0 - FeastySplicingViper: Hydra Edition 🐍🐍🐍

NeoRasp v0.2.0 - FeastySplicingViper: Hydra edition 🐍🐍🐍

The viper learned to break splice2neo into pieces just to put it back together — faster.

What's Changed

• Implemented a scatter gather approach for splice2neo annotation steps.
• Updated documentation to reflect changes.
• Added benchmark directives to monitor ressource consumption.
• Added experimental plotting script to create HTML report of resource usage.

Known Issue(s)

Please note that the scatter size for splice2neo should not be too small. Due to the lack of process safety for BSGenome and GenomicFeatures objects in R, these must be temporarily stored as separate copies per process (chunk), which leads to high disk I/O when processing many small chunks.

Full Changelog: v0.1.0...v0.2.0

v0.0.6 - FeastySplicingViper

NeoRasp v0.0.6 - FeastySplicingViper 🧬🍓🐍

The splicing viper now feasts on two replicates at once — and the buffet just got bigger: tasty mice are now on the menu for neoantigen prediction.

What's Changed

• feat: Add peptide fasta
  • Thanks to @franla23 for raising this issue
• Support for technical replicate
• Updated gene name filter to support mouse as organism
• Updated default resources in workflow profile

Full Changelog: v0.0.5...v0.0.6