feat: update snpeff wrapper

[FelixMoelder]

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

Release Notes

• Chores
  • Upgraded snpEff from 5.2 to 5.3.
  • Refreshed conda environment pins to newer package versions and metadata (security and system library updates).
  • Updated genome/release reference used by the snpEff annotation workflow (release identifier changed).

[coderabbitai]

📝 Walkthrough

Walkthrough

Bumps snpeff from 5.2 → 5.3 in both annotate and download environment.yaml files, refreshes the corresponding linux-64 explicit environment pin files with updated package versions/builds/checksums and conda metadata, and updates two Snakemake parameters in meta/bio/varscan2_snpeff/meta_wrapper.smk (release and snpeff db path).

Changes

Cohort / File(s)	Summary
Conda environment yaml files bio/snpeff/annotate/environment.yaml, bio/snpeff/download/environment.yaml	snpeff dependency bumped from 5.2 → 5.3.
Conda explicit environment pin files (linux-64) bio/snpeff/annotate/environment.linux-64.pin.txt, bio/snpeff/download/environment.linux-64.pin.txt	Full refresh of explicit pins: many packages (ca-certificates, libgomp, libgcc/ng, libstdcxx, openssl, zlib, python_abi, fonts, X11/graphics libs, etc.) updated to newer versions/builds with new URLs and checksums; created-by conda metadata updated from 24.9.2 → 25.9.1.
Snakemake meta wrapper meta/bio/varscan2_snpeff/meta_wrapper.smk	Two parameter literals changed: get_genome_fasta.release 105 → 99; snpeff_annotate input db path resources/snpeff/R64-1-1.105 → resources/snpeff/R64-1-1.99.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20–30 minutes

• Inspect compatibility of snpeff 5.3 with workflows/tests that rely on 5.2.
• Validate the explicit pin updates do not introduce ABI/runtime mismatches (libstdcxx, libgcc, python_abi, openssl).
• Verify the changed Snakemake parameters (release and db path) point to available resources and downstream rules still resolve.

Possibly related PRs

• feat: Varscan2 - SnpEff Meta wrapper #3501 — related changes to varscan2_snpeff meta/wrapper components and tests; high code-level relevance.

Suggested reviewers

• fgvieira
• johanneskoester

Pre-merge checks and finishing touches

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: updating the snpeff wrapper to version 5.3 across multiple environment files and adjusting related parameters.
Description check	✅ Passed	The description follows the template structure and includes all required QC checkboxes marked as complete, confirming adherence to contribution guidelines.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch feat/update_snpeff

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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 d7b04fe and 8bd9517.

📒 Files selected for processing (1)

• meta/bio/varscan2_snpeff/meta_wrapper.smk (2 hunks)

🧰 Additional context used

🧠 Learnings (1)

📚 Learning: 2024-11-26T15:00:09.980Z

Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3502
File: bio/ngsbits/sampleancestry/test/Snakefile:10-11
Timestamp: 2024-11-26T15:00:09.980Z
Learning: For the NGS-bits SampleAncestry wrapper, users should decide which assembly and parameters they want. Supported genome builds are provided through the tool's `url` in `meta.yaml`.

Applied to files:

• meta/bio/varscan2_snpeff/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/varscan2_snpeff/meta_wrapper.smk (1)

10-10: Based on the search results, SnpEff 5.0 provides R64-1-1.75 and R64-1-1.99 databases for Saccharomyces cerevisiae, with no mention of R64-1-1.105. Let me search for SnpEff 5.3 release notes to confirm database availability.

Based on my verification through web searches, I can now provide a conclusive rewritten review comment.

SnpEff 5.3 uses R64-1-1.99 for Saccharomyces cerevisiae; R64-1-1.105 is unavailable.

SnpEff 5.0 provides R64-1-1.75 and R64-1-1.99 databases for Saccharomyces cerevisiae, with R64-1-1.105 not appearing in any documented SnpEff release. SnpEff 5.1+ maintains backward compatibility with 5.0 databases, so SnpEff 5.3 inherits these same available databases. The changes to release 99 (lines 10 and 64) are therefore correct and necessary, as the R64-1-1.105 database does not exist.

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[fgvieira]

See #4578 and #4600.

[FelixMoelder]

See #4578 and #4600.

You are right, but there is also a meta-wrapper which is relying on both snpeff annotate and snpeff download. Therefore it makes sense to update both wrappers in a single PR for the meta-wrapper to be compatible.

[FelixMoelder]

The meta-wrapper uses release version 105 of the reference genome. For some reason this is not part of the snpeff config anymore. The latest release version of the R64-1-1 included in snpeff 5.3 is 99.

[fgvieira]

I have not looked into it too much, but it seems it is because snpeff references moved from Azure to AWS and all URLs are now invalid.

[FelixMoelder]

Actually snpeff behaves weird. In my first comit the tests for snpeff_download and snpeff_annotate passed, while the meta-wrapper was failing due to a outdated reference version. After updating the meta-wrapper the test of snpeff_download failed which does not make sense. According to this comment downloads should be fixed in the latest version.
Locally all tests are passing for me.