fix: write improved consensus variant table as diagnostic output

[m-jahn]

• closes print better formatted table for the consensus variants #48
• closes bcftools intersection has mixed up sample input compared to report #51

[github-actions]

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Language	Validation result
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML_PRETTIER	Pass ✅

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[Copilot]

Copilot review overview

🟡 Changes recommended

A few issues in the updated workflow/report code (misleading consensus file extension, doc path mismatch, unused sample-sheet read, and lingering rowwise grouping) should be fixed to avoid confusion and potential downstream problems.

Review effort: Lite
Findings: 2 · 2

Open (4)

• rowwise grouping is never removed · New
• Consensus output uses misleading .vcf extension · New
• Report text mismatches TSV output path · New
• Unused sample sheet read adds dead I/O · New

What changed in this PR

This PR improves the “consensus variants” diagnostic output used by the report by capturing bcftools isec metadata and expanding the consensus presence/absence encoding into a more user-friendly table (with per-sample columns and variant annotations), addressing the sample-order mismatch described in #51 and the poor formatting in #48.

Changes:

• Update the bcftools intersection rule to use bcftools isec -p output directory artifacts (including README.txt) and wire them into the report inputs.
• Extend the R Markdown report to parse the consensus index, expand the appearance bitstring into named sample columns, annotate variants, and export a TSV alongside the HTML report.
• Minor refactors in report.Rmd (chunk options placement, formatting, and join scope tightening).

File	Description
workflow/​rules/​report.smk	Switch intersection output handling to directory-based isec outputs and pass README.txt into the report step.
workflow/​notebooks/​report.Rmd	Build a richer consensus variant table (sample-named columns + annotations) and write it as a TSV diagnostic output.

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[rabioinf]

looks good!