Release v0.3.0 - FeastySplicingViper: HydrAI edition 🐍🤖🐍 · TRON-Bioinformatics/neorasp

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

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

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)

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