perf: autobump snakemake wrappers

[johanneskoester]

Automated changes by create-pull-request GitHub action

Summary by CodeRabbit

• Chores
  • Upgraded underlying bioinformatics tool versions across the pipeline for improved reliability and consistency: bcftools, samtools, tabix, vembrane, and datavzrd.

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⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 6ea5b9bf-171c-49f8-a6d6-7ac23f5ca7c1

📥 Commits

Reviewing files that changed from the base of the PR and between 0deb304 and 0b089a9.

📒 Files selected for processing (1)

• workflow/rules/annotation.smk

🚧 Files skipped from review as they are similar to previous changes (1)

• workflow/rules/annotation.smk

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📝 Walkthrough

Walkthrough

Bumped Snakemake wrapper/container version strings across multiple rules (download, annotation, eval-results, compare-vcfs, utils). No changes to rule inputs, outputs, parameters, threads, or control flow.

Changes

Cohort / File(s)	Summary
Download rules workflow/rules/download.smk	Updated wrappers: normalize_truth, samtools_faidx, samtools_index from v8.1.1/... → v9.4.1/....
Annotation rules workflow/rules/annotation.smk	Updated wrappers: tabix_revel_scores v8.1.1/bio/tabix/index → v9.4.1/bio/tabix/index; vembrane_table_shared_fn, vembrane_table_unique_fp_fn v7.6.1/bio/vembrane/table → v9.4.0/bio/vembrane/table.
Evaluation / reporting rules workflow/rules/eval-results.smk	Updated wrappers: extract_fp_fn_tp v7.6.1/bio/vembrane/table → v9.4.0/bio/vembrane/table; report_precision_recall, report_fp_fn, report_fp_fn_callset v8.0.3/utils/datavzrd → v9.4.1/utils/datavzrd.
Compare VCFs rules workflow/rules/compare-vcfs.smk	Updated remove_non_pass wrapper for bcftools view from v8.1.1/bio/bcftools/view → v9.4.1/bio/bcftools/view.
Utils rules workflow/rules/utils.smk	Updated norm_vcf wrapper for bcftools norm from v8.1.1/bio/bcftools/norm → v9.4.1/bio/bcftools/norm.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• perf: update tools in conda environments and snakemake wrappers to 7.2.0 #141: Changes the same wrapper declarations (normalize_truth, samtools_faidx/index, remove_non_pass).
• perf: bump snakemake wrappers to v7.8.1 #147: Performs wrapper-version bumps in overlapping Snakemake rules/files (bcftools/samtools wrappers).
• perf: bump snakemake wrappers to v8.0.2 #150: Prior wrapper bump touching the same wrapper references updated here.

Suggested reviewers

• BiancaStoecker

Poem

🐰 I hopped through wrappers, quick and light,
Pushed version bumps into the night.
No logic shifted, just fresher code,
A tidy trail along the road. 🥕

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 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' directly and clearly summarizes the main change: upgrading 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.

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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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