Docs/jl/readme content

[JuliaLienard]

Summary

Creation of the README content and its associated documentation files.

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Type of change

• Bug fix
• Patch / hotfix
• New feature / enhancement
• Refactor / cleanup
• Documentation update

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Checklist (author)

• CHANGELOG updated with a clear entry
• Version bumped in configs/nextflow.hopper.config (if user-facing change, skip if it is an infra only)
• Pipeline runs successfully on stubs (-profile test or equivalent)
• Outputs validated (VCFs, metrics, reports, MultiQC if applicable)
• Output from affected processes inspected (.command.sh, .command.log, .command.err, result files in work/)
• New data formats tested for compatibility with Coyote3
• New data formats tested for compatibility with GENS
• Documentation updated (README, params, examples, usage)
• Containers / tools updated are version-pinned and reproducible
• At least one reviewer has tested and approved the code

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Breaking changes

• No breaking changes
• Params/outputs/configs changed (list details in Summary)
• Output filenames or structure changed (document migration path)

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Testing performed

Describe what was tested, datasets/profiles used, and results. Attach logs or links if helpful.

Performed by:

• Viktor
• Ram
• Sailedra
• Julia

(Add if missing)

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Notes for reviewers

Mention risk areas, edge cases, or anything needing special attention.

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Review performed by

• Viktor
• Ram
• Sailedra

(Add if missing)

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Release notes (draft)

Short, user-facing bullet points for the next release tag.