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Majority rule ensemble approach#276

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kubranarci wants to merge 7 commits intodevfrom
majority-rule-ensemble-approach
Open

Majority rule ensemble approach#276
kubranarci wants to merge 7 commits intodevfrom
majority-rule-ensemble-approach

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@kubranarci
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/variantbenchmarking branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@kubranarci
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@nf-core-bot fix linting

@kubranarci
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@georgiakes This PR requires a bit of attention if you dont mind :) I am introducing a new method which is a common approach to generate a proxy truth set where golden set of truth is not available. The idea is to merge input test VCFs, and keep only common (>n) variants - usually majority. Can you check the logic and text and I have added to see if it makes sense?

Plus, I generated a new metromap looking forward for your comments :)

@kubranarci kubranarci linked an issue Feb 25, 2026 that may be closed by this pull request
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concordance analysis for somatic benchmarking

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