Init test pipeline

[dimalvovs]

This pull request introduces automated testing and container build workflows, refactors the Docker image for improved reproducibility and efficiency, and adds comprehensive test infrastructure for Nextflow modules. The main themes are CI/CD automation, Dockerfile improvements, and Nextflow test support.

CI/CD Automation

• Added .github/workflows/build-push-container.yml to automate building and pushing the Docker image to GitHub Container Registry when relevant files change.
• Added .github/workflows/test.yml to run automated tests on pull requests to main, including setup for Java, Nextflow, and nf-test.

Dockerfile Improvements

• Refactored docker/scratch-annotation.Dockerfile to use a consistent CRAN repository, consolidate system dependencies (including Python, JAGS, HDF5, GSL), streamline R/Bioconductor package installation, and optimize Python environment setup (including CPU-only torch). Removed redundant installs and cleaned up cache handling. [1] [2]

Nextflow Test Infrastructure

• Added nf-test.config and tests/nextflow.config to configure nf-test and container usage for Nextflow module testing. [1] [2]
• Added reusable test data generation process (tests/data/create_data.nf) and R script template (tests/data/templates/make-test-seurat.r) for creating Seurat objects needed in tests. [1] [2]
• Created nf-test test scripts for Azimuth and Sctype modules, including setup, input wiring, and success assertions (tests/modules/local/azimuth/main.nf.test, tests/modules/local/sctype/major/main.nf.test, tests/modules/local/sctype/state/main.nf.test). [1] [2] [3]