perf: update all wrappers to latest wrapper versions with changes

[johanneskoester]

Summary by CodeRabbit

• Chores
  • Upgraded workflow tool wrappers across the pipeline to newer releases, including bcftools, samtools, bedtools, bwa, vg, picard, GATK, freebayes, delly, VEP/annotation, mosdepth, fastp, fastqc, multiqc, sra-tools, tabix, and datavzrd.
  • Updates span modules: annotation, benchmarking, calling, candidate calling, fusion calling, filtering, maf, mapping, primers, QC, references, regions, testcase, trimming, utils, and datavzrd.
  • Notable bumps align many tools to v7.x series.
  • No changes to workflow logic, inputs/outputs, or public interfaces.

[coderabbitai]

Walkthrough

Bulk update of Snakemake wrapper version strings across multiple workflow rule files. Tools (bcftools, samtools, bwa, bedtools, datavzrd, VEP, etc.) are pointed to newer tags; no rule logic, inputs/outputs, or control flow changes. One meta wrapper in fusion_calling switches to a different version line.

Changes

Cohort / File(s)	Summary
Annotation wrappers workflow/rules/annotation.smk	Update VEP/annotation wrapper refs from v3.3.5 to v7.6.0 for three rules.
Benchmarking wrappers workflow/rules/benchmarking.smk	Bump wrapper versions: bcftools/concat, chm-eval-sample, samtools/sort, chm-eval-kit, chm-eval to newer tags.
Variant calling (bcftools) workflow/rules/calling.smk	Update bcftools sort and concat wrappers to v7.6.0.
Candidate calling workflow/rules/candidate_calling.smk	Update wrappers: freebayes, delly, bcftools/filter to newer versions (mainly v7.6.0).
Data visualization (datavzrd, bedtools) workflow/rules/datavzrd.smk	Update utils/datavzrd to v7.6.0 and bedtools/intersect to v7.3.0.
Filtering (bcftools concat) workflow/rules/filtering.smk	Update bcftools concat wrapper to v7.6.0 in two rules.
Fusion calling workflow/rules/fusion_calling.smk	Change meta wrapper to v1.26.0/meta/bio/star_arriba; update bcftools sort/concat to v7.6.0.
MAF conversion workflow/rules/maf.smk	Update bcftools/view wrapper to v7.6.0.
Mapping and preprocessing workflow/rules/mapping.smk	Bump multiple wrappers (bwa, vg, samtools, picard, gatk) to v7.6.0 series.
Primers workflow/rules/primers.smk	Update bwa/mem to v7.6.0 and samtools/view to v7.6.0.
QC workflow/rules/qc.smk	Update fastqc, samtools idxstats/stats, multiqc wrappers to v7.6.0.
Reference assets workflow/rules/ref.smk	Update wrapper versions: ensembl-sequence to v5.10.0, faidx to v7.6.0, ensembl-annotation to v7.4.0, bwa/index to v5.10.0, vep/cache to v7.6.0.
Regions workflow/rules/regions.smk	Update mosdepth wrapper to v7.3.0.
Testcase workflow/rules/testcase.smk	Update bcftools concat to v7.6.0.
Trimming and SRA workflow/rules/trimming.smk	Update fasterq-dump to v7.6.0; fastp to v7.1.0 (SE/PE).
Utilities workflow/rules/utils.smk	Update wrappers: bcftools/view to v7.6.0; samtools/index and tabix/index to v7.3.0.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• perf: update Ensembl wrapper versions in reference rules #386 — Also updates wrapper versions in workflow/rules/ref.smk for Ensembl and VEP-related rules.
• fix: Update datavzrd wrapper #358 — Adjusts datavzrd wrapper versions in workflow/rules/datavzrd.smk.
• feat: annotate access patterns #369 — Modifies annotation wrapper versions in workflow/rules/annotation.smk.

Suggested reviewers

• fxwiegand
• dlaehnemann

Poem

I twitched my nose at version strings,
Hop-hop through rules and wrapper things.
New tags sprout like fields of green,
Same old paths, just fresher sheen.
With gentle thumps I sign this feat—
All carrots aligned, the pipeline neat. 🥕🐇

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 succinctly describes the main purpose of the PR—updating all Snakemake wrapper versions to their latest releases—and accurately reflects the changeset without unrelated detail.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch perf/wrapper-update-specific

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[coderabbitai]

Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between ee49828 and 6717acf.

📒 Files selected for processing (16)

• workflow/rules/annotation.smk (3 hunks)
• workflow/rules/benchmarking.smk (5 hunks)
• workflow/rules/calling.smk (2 hunks)
• workflow/rules/candidate_calling.smk (3 hunks)
• workflow/rules/datavzrd.smk (4 hunks)
• workflow/rules/filtering.smk (2 hunks)
• workflow/rules/fusion_calling.smk (3 hunks)
• workflow/rules/maf.smk (1 hunks)
• workflow/rules/mapping.smk (11 hunks)
• workflow/rules/primers.smk (2 hunks)
• workflow/rules/qc.smk (4 hunks)
• workflow/rules/ref.smk (5 hunks)
• workflow/rules/regions.smk (1 hunks)
• workflow/rules/testcase.smk (1 hunks)
• workflow/rules/trimming.smk (3 hunks)
• workflow/rules/utils.smk (3 hunks)

⏰ 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). (7)

• GitHub Check: test target regions
• GitHub Check: test sra download
• GitHub Check: test local input
• GitHub Check: test primers
• GitHub Check: test testcase generation
• GitHub Check: test target regions, multiple BEDs
• GitHub Check: test no candidate filtering

🔇 Additional comments (20)

workflow/rules/testcase.smk (1)

17-17: LGTM! Wrapper version update.

The bcftools/concat wrapper version update from v2.3.2 to v7.6.0 is straightforward with no changes to rule logic or parameters.

workflow/rules/filtering.smk (1)

65-65: LGTM! Wrapper version updates.

The bcftools/concat wrapper version updates to v7.6.0 in both gather_calls and merge_calls rules are straightforward with no changes to rule logic or parameters.

Also applies to: 95-95

workflow/rules/regions.smk (1)

49-49: LGTM! Wrapper version update.

The mosdepth wrapper version update from v2.3.2 to v7.3.0 is straightforward with no changes to rule logic or parameters.

workflow/rules/qc.smk (1)

12-12: LGTM! Wrapper version updates.

The wrapper version updates to v7.6.0 for fastqc, samtools/idxstats, samtools/stats, and multiqc are straightforward with no changes to rule logic or parameters.

Also applies to: 24-24, 35-35, 53-53

workflow/rules/annotation.smk (1)

24-24: LGTM! Wrapper version updates.

The wrapper version updates to v7.6.0 for vep/annotate (in annotate_candidate_variants and annotate_variants) and bcftools/concat (in gather_annotated_calls) are straightforward with no changes to rule logic or parameters.

Also applies to: 52-52, 117-117

workflow/rules/trimming.smk (1)

8-8: LGTM! Wrapper version updates.

The wrapper version updates for sra-tools/fasterq-dump (v7.6.0) and fastp (v7.1.0 in both SE and PE rules) are straightforward with no changes to rule logic or parameters.

Also applies to: 39-39, 59-59

workflow/rules/primers.smk (1)

62-62: LGTM! Wrapper version updates.

The wrapper version updates to v7.6.0 for bwa/mem (in map_primers) and samtools/view (in filter_unmapped_primers) are straightforward with no changes to rule logic or parameters.

Also applies to: 75-75

workflow/rules/mapping.smk (1)

13-13: Approve wrapper version updates
All v7.6.0 wrappers exist in the Snakemake wrappers repository. Please confirm that the workflow’s test suite (or a representative run) has been executed to validate compatibility and detect any breaking changes.

workflow/rules/candidate_calling.smk (1)

23-23: LGTM! Wrapper version upgrades are consistent.

The wrapper versions have been upgraded to v7.6.0 for freebayes, delly, and bcftools/filter, aligning with the PR's objective to update to the latest wrapper versions.

Also applies to: 41-41, 70-70

workflow/rules/datavzrd.smk (2)

106-106: LGTM! Datavzrd wrapper upgrades are consistent.

The datavzrd wrapper has been upgraded from v6.2.0 to v7.6.0 across all three rules (datavzrd_variants_calls, datavzrd_fusion_calls, datavzrd_coverage).

Also applies to: 144-144, 198-198

---

159-159: LGTM! Bedtools wrapper upgrade is consistent.

The bedtools/intersect wrapper has been upgraded from v2.6.0 to v7.3.0.

workflow/rules/calling.smk (1)

111-111: LGTM! Bcftools wrapper upgrades are consistent.

Both bcftools wrappers (sort and concat) have been upgraded to v7.6.0, aligning with the PR's objective.

Also applies to: 125-125

workflow/rules/utils.smk (1)

22-22: LGTM! Tool wrapper upgrades are consistent.

The wrapper versions have been upgraded for bcftools/view (v7.6.0), samtools/index (v7.3.0), and tabix/index (v7.3.0).

Also applies to: 33-33, 47-47

workflow/rules/maf.smk (1)

9-9: LGTM! Bcftools/view wrapper upgrade is consistent.

The wrapper has been upgraded from v3.8.0 to v7.6.0.

workflow/rules/fusion_calling.smk (1)

98-98: LGTM! Bcftools wrapper upgrades are consistent.

Both bcftools wrappers (sort and concat) have been upgraded from v1.21.0 to v7.6.0.

Also applies to: 116-116

workflow/rules/ref.smk (3)

26-26: LGTM! Clear wrapper upgrades are consistent.

The samtools/faidx and vep/cache wrappers have been upgraded to v7.6.0.

Also applies to: 137-137

---

123-123: Verify the bwa/index wrapper version.

The wrapper version changes from v2.3.2 to v5.10.0. While this appears to be an upgrade, it's a significant jump. Please confirm this is the latest stable version.

---

14-14: Verify ensembl wrapper version downgrades

• ensembl-sequence: v7.3.0 → v5.10.0
• ensembl-annotation: v7.5.0 → v7.4.0

These are older than the latest available tags (up to v7.6.1); confirm these downgrades are intentional.

workflow/rules/benchmarking.smk (2)

16-16: LGTM! Major wrapper upgrades are consistent.

The wrapper versions have been upgraded for bcftools/concat (v7.6.0), chm-eval-sample (v7.3.0), and samtools/sort (v7.6.0).

Also applies to: 26-26, 40-40

---

68-68: LGTM! CHM-eval wrapper upgrades are consistent.

Both chm-eval wrappers (chm-eval-kit and chm-eval) have been upgraded from v2.3.2 to v2.9.1.

Also applies to: 114-114