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Always run all SV callers #542

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@fellen31 fellen31 commented Jan 21, 2025

In addition, add a hidden parameter to publish_unannotated_svs_and_cnvs_per_family_and_caller. The files will be output as svs/family/${family_id}/${family_id}_${caller}_svs.vcf.gz and cnvs/family/${family_id}/${family_id}_hificnv_cnvs.vcf.gz.

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).

@fellen31 fellen31 linked an issue Jan 21, 2025 that may be closed by this pull request
@fellen31 fellen31 marked this pull request as ready for review January 22, 2025 16:21
@fellen31 fellen31 requested a review from a team as a code owner January 22, 2025 16:21
@fellen31 fellen31 marked this pull request as draft January 24, 2025 14:07
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Possibility to run more than one SV-caller
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