perf: autobump snakemake wrappers

[johanneskoester]

Automated changes by create-pull-request GitHub action

Summary by CodeRabbit

• Chores
  • Updated workflow bioinformatics tool versions (VEP, bcftools, picard markduplicates, mosdepth) to latest stable releases for improved performance, compatibility, and access to recent tool improvements.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: c80e39ca-e5b3-4f96-a4b0-24d1a8c1b457

📥 Commits

Reviewing files that changed from the base of the PR and between 42d47b1 and 5440eb0.

📒 Files selected for processing (4)

• workflow/rules/annotation.smk
• workflow/rules/compare-vcfs.smk
• workflow/rules/download.smk
• workflow/rules/utils.smk

✅ Files skipped from review due to trivial changes (1)

• workflow/rules/download.smk

🚧 Files skipped from review as they are similar to previous changes (2)

• workflow/rules/utils.smk
• workflow/rules/compare-vcfs.smk

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📝 Walkthrough

Walkthrough

This PR updates only Snakemake wrapper version strings across rules for VEP annotation, bcftools index/sort, Picard markduplicates, and mosdepth; no rule inputs, outputs, params, logs, or control flow were changed.

Changes

Wrapper version bumps

Layer / File(s)	Summary
VEP annotation rules workflow/rules/annotation.smk	Updated VEP cache wrapper to v9.4.2/bio/vep/cache and VEP annotate wrappers to v9.8.0/bio/vep/annotate.
BCFtools index & sort workflow/rules/utils.smk, workflow/rules/compare-vcfs.smk	Updated bcftools index and sort wrappers from v8.1.1 to v9.4.2 for VCF/BCF indexing and sorting rules.
Download / processing tools workflow/rules/download.smk	Bumped mark_duplicates wrapper to v9.4.2/bio/picard/markduplicates and mosdepth to v9.8.0/bio/mosdepth.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Possibly related PRs

• snakemake-workflows/dna-seq-benchmark#154: Overlaps edits to VEP annotation rules in workflow/rules/annotation.smk.
• snakemake-workflows/dna-seq-benchmark#150: Similar wrapper version bumps across bcftools-related rules and overlapping files.
• snakemake-workflows/dna-seq-benchmark#147: Also updates wrapper version strings for bcftools and related workflow rules.

Suggested reviewers

• famosab
• BiancaStoecker

Poem

🐰 A tiny bump, a tag anew,
Wrappers align, the lines stay true.
VEP and bcftools step up the game,
Picard and mosdepth join the same,
Hops of version joy — a rabbit’s refrain!

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'perf: autobump snakemake wrappers' clearly and specifically summarizes the main change: updating Snakemake wrapper versions across multiple workflow rules for performance improvements.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch perf/autobump-wrappers

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