perf: autobump snakemake wrappers #155
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📝 WalkthroughWalkthroughThe pull request updates Snakemake wrapper version references across four workflow rule files, upgrading bcftools wrappers from v8.0.2 to v8.1.1, datavzrd from v8.0.2 to v8.0.3, and other tool wrappers to v5.10.0 where applicable. No control flow or functional logic changes. Changes
Estimated code review effort🎯 1 (Trivial) | ⏱️ ~3 minutes Possibly related PRs
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🧰 Additional context used🧠 Learnings (1)📚 Learning: 2025-11-11T08:47:27.118ZApplied to files:
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🔇 Additional comments (4)
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⚠️ Outside diff range comments (1)
workflow/rules/download.smk (1)
268-268: Update mosdepth wrapper to v8.1.1.The mosdepth wrapper at Line 268 remains at v8.0.2 while other bio wrappers in this file have been updated to v8.1.1 (bcftools/norm, samtools/faidx, bwa/mem, picard/markduplicates, samtools/index). Align mosdepth to v8.1.1 to be consistent with the rest of the updates.
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📒 Files selected for processing (4)
workflow/rules/compare-vcfs.smkworkflow/rules/download.smkworkflow/rules/eval-results.smkworkflow/rules/utils.smk
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🧠 Learnings (1)
📚 Learning: 2025-11-11T08:47:27.118Z
Learnt from: BiancaStoecker
Repo: snakemake-workflows/dna-seq-benchmark PR: 149
File: workflow/Snakefile:36-40
Timestamp: 2025-11-11T08:47:27.118Z
Learning: In the dna-seq-benchmark workflow, VCF files are sorted by a generic sort_vcf rule in workflow/rules/utils.smk that transforms {prefix}.vcf.gz to {prefix}.sorted.vcf.gz, so rules that produce VCF outputs don't include .sorted in their filenames - the sorting is handled as a separate downstream step.
Applied to files:
workflow/rules/compare-vcfs.smkworkflow/rules/utils.smk
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🔇 Additional comments (4)
workflow/rules/compare-vcfs.smk (1)
115-115: LGTM! Consistent bcftools wrapper updates.The bcftools wrapper updates from v8.0.2 to v8.1.1 are consistent with the updates in
workflow/rules/utils.smk. The verification requested for that file will cover these changes as well.Also applies to: 211-211
workflow/rules/utils.smk (1)
9-9: bcftools wrapper v8.1.1 versions verified and available.The wrapper versions v8.1.1 for bcftools/index and bcftools/sort are available in the snakemake-wrappers repository and accessible.
workflow/rules/eval-results.smk (1)
84-84: The datavzrd wrapper v8.0.3 is available in the snakemake-wrappers repository. All three updates at lines 84, 266, and 296 are consistent and properly implemented.workflow/rules/download.smk (1)
94-94: All wrapper versions are available and valid.Verified that all updated wrappers exist in the snakemake-wrappers repository:
- v8.1.1: bio/bcftools/norm, bio/samtools/faidx, bio/bwa/mem, bio/picard/markduplicates, bio/samtools/index
- v5.10.0: bio/reference/ensembl-sequence, bio/bwa/index
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