fix: update vep wrappers to 8.0.0 to make env installable

[famosab]

Summary by CodeRabbit

• Chores
  • Updated Variant Effect Predictor (VEP) tooling to v8.0.0, including annotation, cache, and plugin wrappers for more current, compatible reference/annotation behavior.

[coderabbitai]

Walkthrough

Wrapper version strings for VEP were updated to v8.0.0 in four Snakemake rules across two workflow files; no other logic, inputs/outputs, or control flow were changed.

Changes

Cohort / File(s)	Summary
Annotation rule wrapper updates workflow/rules/annotation.smk	Rules annotate_candidate_variants and annotate_variants wrapper version changed from v7.6.0/bio/vep/annotate → v8.0.0/bio/vep/annotate.
Reference rule wrapper updates workflow/rules/ref.smk	Rules get_vep_cache updated v7.6.0/bio/vep/cache → v8.0.0/bio/vep/cache; get_vep_plugins updated v7.7.0/bio/vep/plugins → v8.0.0/bio/vep/plugins.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

• Homogeneous version bumps without logic changes.
• Files to spot-check: workflow/rules/annotation.smk, workflow/rules/ref.smk to confirm wrapper strings and any surrounding context (comments/inputs) remain consistent.

Possibly related PRs

• perf: update vep wrappers #401 — Updates VEP wrapper versions across the same annotation and reference rules.
• perf: update Ensembl wrapper versions in reference rules #386 — Modifies VEP wrapper references in workflow/rules/ref.smk for cache/plugins.
• feat: annotate access patterns #369 — Alters annotation rules in workflow/rules/annotation.smk (related to VEP annotation rules).

Suggested reviewers

• fxwiegand
• johanneskoester

Poem

🐰
I hopped through rules with nimble feet,
Swapped VEP strings to make them neat.
v8.0.0 whispered, "Now we're new,"
Variants hop on, lined up in queue —
A tiny rabbit clap for CI's beat.

Pre-merge checks and finishing touches

✅ 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 accurately describes the main changes: updating VEP wrapper versions from 7.6.0/7.7.0 to 8.0.0 across multiple rules to resolve installation issues.
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

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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 3118010 and 9193c2c.

📒 Files selected for processing (2)

• workflow/rules/annotation.smk (2 hunks)
• workflow/rules/ref.smk (2 hunks)

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

• workflow/rules/annotation.smk
• workflow/rules/ref.smk

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

workflow/rules/ref.smk (1)

137-137: Consider updating to v8.8.0 for consistency.

The cache wrapper is updated to v8.0.0 while the plugins wrapper (line 148) and both annotate wrappers (workflow/rules/annotation.smk:24,52) are updated to v8.8.0. Is there a specific reason for keeping the cache at v8.0.0?

If v8.8.0 is available for the cache wrapper and compatible, consider updating for version consistency:

-        "v8.0.0/bio/vep/cache"
+        "v8.8.0/bio/vep/cache"

Alternatively, verify that v8.0.0 cache is compatible with v8.8.0 annotate/plugins wrappers.

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between c75e4b2 and 3118010.

📒 Files selected for processing (2)

• workflow/rules/annotation.smk (2 hunks)
• workflow/rules/ref.smk (2 hunks)

🧰 Additional context used

🧠 Learnings (1)

📚 Learning: 2024-11-25T12:34:09.018Z

Learnt from: johanneskoester
Repo: snakemake-workflows/dna-seq-varlociraptor PR: 338
File: workflow/rules/candidate_calling.smk:86-87
Timestamp: 2024-11-25T12:34:09.018Z
Learning: In this workflow, the grouping of variant calling rules is intentional, and not all related variant calling rules need to be grouped under "calling".

Applied to files:

• workflow/rules/annotation.smk

🔇 Additional comments (2)

workflow/rules/annotation.smk (1)

52-52: Consistent with the other annotation rule.

Both VEP annotation rules now use v8.8.0, which maintains consistency.

workflow/rules/ref.smk (1)

148-148: Version update looks good.

The plugins wrapper is updated to v8.8.0, consistent with the annotate wrappers.