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Liftover to sniffles nf-core module #313

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Liftover to sniffles nf-core module #313

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@nourmahfel
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PR checklist

  • This comment contains a description of changes (with reason).
    Replaced the local implementation of Sniffles with the standard nf-core/sniffles module to improve modularity and maintain consistency with nf-core best practices. Updated the subworkflow (structural_variant_calling.nf) to call the new module and commented out the local sniffles.nf process.
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • CHANGELOG.md is updated.

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @nourmahfel,

It looks like this pull-request is has been made against the nourmahfel/nanoseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nourmahfel/nanoseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@nourmahfel nourmahfel changed the base branch from master to dev March 25, 2025 15:19
@nourmahfel nourmahfel marked this pull request as draft March 26, 2025 11:39
nourmahfel
nourmahfel commented Mar 26, 2025
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Updated the sniffles module to nf-core

@nourmahfel nourmahfel marked this pull request as ready for review March 26, 2025 11:47
@nourmahfel nourmahfel requested a review from yuukiiwa March 26, 2025 11:49
@nourmahfel nourmahfel closed this Mar 26, 2025
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@nourmahfel