perf: Update alignoth report meta wrapper

[fxwiegand]

QC

• I confirm that I have followed the documentation for contributing to snakemake-wrappers.

While the contributions guidelines are more extensive, please particularly ensure that:

• test.py was updated to call any added or updated example rules in a Snakefile
• input: and output: file paths in the rules can be chosen arbitrarily
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
• the meta.yaml contains a link to the documentation of the respective tool or command under url:
• conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• Chores
  • Updated alignoth tool to the latest version for improved compatibility and performance improvements.

[coderabbitai]

📝 Walkthrough

Walkthrough

A Snakemake wrapper reference for the alignoth rule is updated from version v8.0.1 to v8.0.2 in a single wrapper configuration file, with no changes to rule logic or error handling.

Changes

Cohort / File(s)	Summary
Wrapper version bump meta/bio/alignoth_report/meta_wrapper.smk	Updated Snakemake wrapper reference from v8.0.1/bio/alignoth to v8.0.2/bio/alignoth

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Possibly related PRs

• perf: Update alignoth wrapper #4728: Concurrently bumps the alignoth package version to 1.4.1 alongside this wrapper version update
• perf: Update alignoth report meta wrapper #4717: Previously modified the same wrapper file to bump version to v8.0.1, which is now being updated to v8.0.2
• perf: Update alignoth wrapper #4715: Updates the alignoth wrapper's environment and package dependencies (alignoth 1.3.0 → 1.4.0) complementing this wrapper reference bump

Suggested reviewers

• johanneskoester

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description check	⚠️ Warning	The PR description contains only the template boilerplate with unchecked QC boxes and no actual description of the changes made or rationale provided.	Add a meaningful description of what was changed, why it was changed, and any relevant details about the version update (e.g., from v8.0.1 to v8.0.2) and its justification.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title follows conventional commit style (perf: ...) and accurately describes the main change: updating the alignoth report meta wrapper version.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fxwiegand-patch-2

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📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 146dcc0 and 620c8b5.

📒 Files selected for processing (1)

• meta/bio/alignoth_report/meta_wrapper.smk (1 hunks)

🧰 Additional context used

🧠 Learnings (3)

📓 Common learnings

Learnt from: dlaehnemann
Repo: snakemake/snakemake-wrappers PR: 3115
File: CHANGELOG.md:5-5
Timestamp: 2024-10-08T17:41:54.542Z
Learning: Do not review release-please commits in the Snakemake wrappers repository as they are auto-formatted.

Learnt from: dlaehnemann
Repo: snakemake/snakemake-wrappers PR: 3115
File: CHANGELOG.md:5-5
Timestamp: 2024-08-14T15:21:37.230Z
Learning: Do not review release-please commits in the Snakemake wrappers repository as they are auto-formatted.

Learnt from: johanneskoester
Repo: snakemake/snakemake-wrappers PR: 3478
File: bio/varlociraptor/estimate-alignment-properties/test/Snakefile:11-12
Timestamp: 2024-11-15T18:32:07.612Z
Learning: In the `snakemake-wrappers` repository, when developing wrappers, it's acceptable to use "master" as the wrapper version in the `wrapper` directive. This ensures that the documentation always reflects the latest stable version of the wrappers.

Learnt from: johanneskoester
Repo: snakemake/snakemake-wrappers PR: 3478
File: bio/varlociraptor/estimate-alignment-properties/wrapper.py:5-12
Timestamp: 2024-11-21T10:23:03.427Z
Learning: In the Snakemake wrappers project, avoid suggesting extensive error handling or temporary file management in simple wrapper scripts when it may be unnecessary, to prevent overcomplicating the code.

Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3496
File: bio/mtnucratio/wrapper.py:27-28
Timestamp: 2024-11-26T08:30:23.818Z
Learning: In Snakemake wrappers (e.g., `wrapper.py` files), it's unnecessary to verify the availability of tools like `mtnucratio` within the code, because Snakemake with Conda ensures that the required tools are installed and available.

Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3501
File: meta/bio/varscan2_snpeff/test/Snakefile:1-10
Timestamp: 2024-11-26T10:49:04.406Z
Learning: In the `snakemake-wrappers` project, it's acceptable to use "master" in the wrapper path instead of pinning to a specific version.

Learnt from: johanneskoester
Repo: snakemake/snakemake-wrappers PR: 3478
File: bio/varlociraptor/preprocess-variants/wrapper.py:0-0
Timestamp: 2024-11-15T13:48:33.759Z
Learning: In Snakemake wrappers, security considerations like input sanitization are unnecessary, as the wrappers are under full control of the user.

📚 Learning: 2024-11-15T18:32:07.612Z

Learnt from: johanneskoester
Repo: snakemake/snakemake-wrappers PR: 3478
File: bio/varlociraptor/estimate-alignment-properties/test/Snakefile:11-12
Timestamp: 2024-11-15T18:32:07.612Z
Learning: In the `snakemake-wrappers` repository, when developing wrappers, it's acceptable to use "master" as the wrapper version in the `wrapper` directive. This ensures that the documentation always reflects the latest stable version of the wrappers.

Applied to files:

• meta/bio/alignoth_report/meta_wrapper.smk

📚 Learning: 2024-11-21T10:23:03.427Z

Learnt from: johanneskoester
Repo: snakemake/snakemake-wrappers PR: 3478
File: bio/varlociraptor/estimate-alignment-properties/wrapper.py:5-12
Timestamp: 2024-11-21T10:23:03.427Z
Learning: In the Snakemake wrappers project, avoid suggesting extensive error handling or temporary file management in simple wrapper scripts when it may be unnecessary, to prevent overcomplicating the code.

Applied to files:

• meta/bio/alignoth_report/meta_wrapper.smk

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (3)

• GitHub Check: docs
• GitHub Check: testing
• GitHub Check: Summary

🔇 Additional comments (1)

meta/bio/alignoth_report/meta_wrapper.smk (1)

40-40: Wrapper version v8.0.2 is valid and contains the expected performance improvement.

Verification confirms that v8.0.2 exists in the snakemake-wrappers repository and includes performance improvements from upgrading alignoth 1.4.0 → 1.4.1 and libopenblas dependencies. The wrapper code remains unchanged; only the environment dependencies were updated. No breaking changes identified.

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