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Update to nf-core concat#260

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LouisLeNezet wants to merge 4 commits intonf-core:devfrom
LouisLeNezet:sbwf_concat
Open

Update to nf-core concat#260
LouisLeNezet wants to merge 4 commits intonf-core:devfrom
LouisLeNezet:sbwf_concat

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@LouisLeNezet
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@LouisLeNezet LouisLeNezet commented Mar 9, 2026

PR checklist

The change in md5sum for beagle5 vcf is due to the use of the --ligate option that tries to keep the phase.
This induce tiny change in the output hence the change in the variantsMD5.

  • 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/phaseimpute 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.

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