feat: add rule-specific container configuration option (#30)

[radusuciu]

This PR adds a resource configuration item aws_batch_container_image that can be used to customize the container any given rule uses when running on AWS Batch. As discussed in #30 and #31, currently it's possible to specify a container image that every rule in a workflow uses, and if you want to run an individual rule in a different container you have use apptainer, with some extra hoops if you need to authenticate with a private registry (eg. ECR).

There is a bit of a catch however - you need to base your image on the snakemake docker image. I don't think this is something that would be easy to work around and probably not a good fit with snakemake's design. I can update the documentation if this is going to be merged.

Summary by CodeRabbit

Release Notes

• New Features

  • Rules can now specify custom container images on a per-rule basis to override the global default configuration, enabling use of specialized containers for different workloads.

• Documentation

  • Added documentation explaining how to configure rule-specific container images with examples.

[coderabbitai]

📝 Walkthrough

Walkthrough

Implements per-rule container image overrides for AWS Batch jobs via an aws_batch_container_image resource parameter. When specified per-rule, this parameter takes precedence over the global container image configuration. Includes documentation describing the feature and usage example.

Changes

Cohort / File(s)	Summary
Documentation docs/further.md	Adds "Rule-Specific Container Images" section documenting the new aws_batch_container_image resource parameter, including usage example and explanation of per-rule container customization.
Implementation snakemake_executor_plugin_aws_batch/__init__.py	Implements per-rule container image override by computing container_image from job.resources["aws_batch_container_image"] if present, otherwise falling back to self.container_image, and passing the computed value to BatchJobBuilder.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

• Specific areas to review:
  • Verify the fallback logic correctly prioritizes rule-specific aws_batch_container_image over the global self.container_image
  • Confirm job.resources access is safe and handles missing keys appropriately
  • Validate that BatchJobBuilder correctly receives and uses the computed container_image parameter

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run @coderabbitai generate docstrings to improve docstring coverage.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main change: adding a rule-specific container configuration option. This directly aligns with the primary purpose of the PR, which introduces per-rule container image customization via the aws_batch_container_image resource parameter.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

docs/further.md (1)

31-48: Consider documenting the container image constraint.

The documentation clearly explains the feature and provides a helpful example. However, per the PR description, custom container images must be based on the Snakemake Docker image. Consider adding a note about this constraint to help users avoid runtime errors.

Example addition:

 This allows you to use different containers with specialized tools for different rules within the same workflow, rather than requiring all tools to be present in a single container.
+
+**Note:** Custom container images must be based on the Snakemake Docker image to ensure compatibility with the executor plugin's job execution requirements.

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 2525ca0 and 2334d44.

📒 Files selected for processing (2)

• docs/further.md (1 hunks)
• snakemake_executor_plugin_aws_batch/__init__.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

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Files:

• snakemake_executor_plugin_aws_batch/__init__.py

🧬 Code graph analysis (1)

snakemake_executor_plugin_aws_batch/__init__.py (1)

snakemake_executor_plugin_aws_batch/batch_job_builder.py (1)

• BatchJobBuilder (14-136)

🔇 Additional comments (1)

snakemake_executor_plugin_aws_batch/__init__.py (1)

135-145: LGTM! Clean implementation of per-rule container image override.

The implementation correctly retrieves the rule-specific container image from job resources with a proper fallback to the global container image. The use of dict.get() with a default value is the appropriate pattern, and the integration with BatchJobBuilder is correct.