feat: added pixi env, test tasks, and updated apptainer workflow to handle new --containerize args

[m-jahn]

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Pull request overview

Adds a Pixi-managed environment and a small Snakemake-based test fixture to validate workflow execution and Apptainer containerization, and updates the Apptainer deployment workflow to use the new --containerize argument handling.

Changes:

• Add pixi.toml + pixi.lock with tasks to run test workflow/containerization and build an Apptainer image.
• Add a minimal .test/ Snakemake project (Snakefile, env YAML, sample FASTQ) to exercise conda + wrapper execution.
• Update .github/workflows/deploy-apptainer.yml to generate an Apptainer recipe via a GitHub Action input (containerize-args) instead of Dockerfile→def conversion.

Reviewed changes

Copilot reviewed 6 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
pixi.toml	Defines the Pixi workspace, dependencies, and local tasks for running Snakemake tests/containerization.
pixi.lock	Pins the Pixi environment for reproducible CI/local runs.
.test/Snakefile	Minimal test workflow including conda usage and a wrapper invocation.
.test/test_env.yaml	Minimal conda env used by the test rule.
.test/input.fastq	Sample input used by the wrapper test rule.
.gitignore	Ignores Snakemake/Pixi artifacts produced by local/CI runs.
.github/workflows/deploy-apptainer.yml	Updates the deployment workflow to rely on containerize args support.
.gitattributes	Marks pixi.lock as generated / non-diff / binary-merge to reduce noise and merge conflicts.

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[m-jahn]

Note: Do not merge this PR until the upstream dependency www.github.com/snakemake/snakemake-github-action is fixed. After that, this section in deploy-apptainer.yaml must be updated.

      - name: create apptainer recipe
        uses: m-jahn/snakemake-github-action@fix_apptainer
        with:

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