perf: update snakemake wrappers to 7.0.0

[famosab]

Summary by CodeRabbit

• Chores
  • Updated bioinformatics tools for genome indexing, alignment, duplicate marking, and variant evaluation to newer versions for improved reliability.
  • Improved logging organization for genome indexing.
  • Enhanced alignment parameters with additional read group information.
  • Optimized caching behavior and specified thread usage for certain processing steps.

[coderabbitai]

Walkthrough

Multiple Snakemake rules across download, eval, and utils workflows were updated to use newer wrapper versions (mostly v7.0.0). The get_reference rule added a cache directive, bwa_mem added an extra parameter for read groups, bwa_index changed its log file path, and some rules added explicit thread counts. No other inputs, outputs, or control flow were changed.

Changes

File(s)	Change Summary
workflow/rules/download.smk	Updated multiple wrapper versions to v7.0.0; added cache: "omit-software" to get_reference; changed bwa_index log path; added extra parameter to bwa_mem; added threads: 4 to samtools_index and mosdepth
workflow/rules/eval.smk	Updated wrapper versions for remove_non_pass, index_stratified_truth, and reporting rules to v7.0.0
workflow/rules/utils.smk	Updated wrapper versions for index_vcf and index_bcf to v7.0.0

Poem

🐇 Hopping forward, wrappers anew,
BWA and Picard, versions grew!
Logs now nested, groups in line,
Pipelines run smooth, all works fine.
A rabbit’s touch, precise and bright,
Keeping workflows hopping light! 🌿✨

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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 ab2660a and 9476183.

📒 Files selected for processing (3)

• workflow/rules/download.smk (8 hunks)
• workflow/rules/eval.smk (5 hunks)
• workflow/rules/utils.smk (2 hunks)

✅ Files skipped from review due to trivial changes (2)

• workflow/rules/utils.smk
• workflow/rules/eval.smk

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

• workflow/rules/download.smk

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