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adding aardvark benchmarking - #315

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kubranarci merged 13 commits into
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add-aardvark-tool
Jul 20, 2026
Merged

adding aardvark benchmarking#315
kubranarci merged 13 commits into
devfrom
add-aardvark-tool

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@kubranarci

@kubranarci kubranarci commented Jul 15, 2026

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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).

@kubranarci kubranarci linked an issue Jul 17, 2026 that may be closed by this pull request
add aardvark to the available benchmark tools #314
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@kubranarci
kubranarci requested a review from georgiakes July 17, 2026 12:52
georgiakes
georgiakes reviewed Jul 17, 2026
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@georgiakes georgiakes left a comment

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Hellooo. Here are some comments :)

georgiakes
georgiakes requested changes Jul 17, 2026
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Comment thread assets/schema_input.json
Comment thread assets/samplesheet_HG008.csv Outdated
Comment thread conf/tests/somatic_small.config
Comment thread docs/usage.md Outdated
Comment thread CHANGELOG.md Outdated
georgiakes
georgiakes reviewed Jul 17, 2026
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Comment thread conf/tests/germline_small.config Outdated
kubranarci and others added 3 commits July 20, 2026 09:39
@kubranarci @georgiakes
Update docs/usage.md
3d63707 
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
@kubranarci @georgiakes
Update conf/tests/germline_small.config
ed494ef 
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
@kubranarci
resolve comments
71f2667
@kubranarci

kubranarci commented Jul 20, 2026

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@nf-core-bot fix linting

@kubranarci
kubranarci requested a review from georgiakes July 20, 2026 08:28
georgiakes
georgiakes reviewed Jul 20, 2026
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Comment thread assets/schema_input.json
georgiakes
georgiakes reviewed Jul 20, 2026
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Comment thread subworkflows/local/prepare_vcfs_test/main.nf Outdated
georgiakes
georgiakes reviewed Jul 20, 2026
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Comment thread docs/usage.md
@kubranarci

kubranarci commented Jul 20, 2026

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@nf-core-bot fix linting

georgiakes
georgiakes approved these changes Jul 20, 2026
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LGTM!

@kubranarci
kubranarci merged commit 1d3fb18 into dev Jul 20, 2026
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@kubranarci
kubranarci deleted the add-aardvark-tool branch July 23, 2026 12:31
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add aardvark to the available benchmark tools

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