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feat(cutesv): add optional regions input - #13502

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awgymer:cutesv-include-bed
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feat(cutesv): add optional regions input#13502
awgymer wants to merge 1 commit into
nf-core:masterfrom
awgymer:cutesv-include-bed

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@awgymer awgymer commented Oct 30, 2026 •
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Add support for a regions bed to filter calling regions to cuteSV. This is passed via the -include-bed option

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!
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test cutesv --profile docker
      • nf-core modules test cutesv --profile singularity
      • nf-core modules test cutesv --profile conda

@awgymer
feat(cutesv): add optional regions input
639d02c 
Add an optional regions BED file to the input tuple. The module gives
the file to cuteSV with -include_bed. Add a test that shows that the
module calls only the SVs in the regions.
@awgymer
awgymer marked this pull request as ready for review October 30, 2026 04:20
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