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[BF][ENH] Harmonization works better now - #124

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arnaudbore merged 8 commits into
scilus:devfrom
arnaudbore:fix_harmonisation_and_validation
Sep 3, 2026
Merged

arnaudbore merged 8 commits into
scilus:devfrom
arnaudbore:fix_harmonisation_and_validation

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@arnaudbore

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  • Add params to handle harmonization
  • default value if handedness or sex not provided
  • check if enough subjects to run harmonization

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
  • 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).

@arnaudbore
arnaudbore requested a review from Manonedde August 31, 2026 15:19
@AlexVCaron

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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: 3.5.2.
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.

@Manonedde Manonedde left a comment

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It just occurred to me that I don't see the model listed as a parameter, given that clinical-combat also includes pairwise (the linear version of clinical). Do we want to require the use of clinical, or allow users to switch to pairwise?

Comment thread nextflow_schema.json Outdated
Comment thread nextflow_schema.json Outdated
Comment thread nextflow_schema.json Outdated
Comment thread nextflow_schema.json Outdated
arnaudbore and others added 5 commits September 3, 2026 09:52
Co-authored-by: Manon Edde <60670074+Manonedde@users.noreply.github.com>
Co-authored-by: Manon Edde <60670074+Manonedde@users.noreply.github.com>
Co-authored-by: Manon Edde <60670074+Manonedde@users.noreply.github.com>
Co-authored-by: Manon Edde <60670074+Manonedde@users.noreply.github.com>
@arnaudbore
arnaudbore merged commit 045f6af into scilus:dev Sep 3, 2026
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3 participants