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Bump CuteSV version#11052

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awgymer wants to merge 1 commit intonf-core:masterfrom
awgymer:update-cutesv
Open

Bump CuteSV version#11052
awgymer wants to merge 1 commit intonf-core:masterfrom
awgymer:update-cutesv

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@awgymer awgymer commented Mar 26, 2026

Bumps the tool version from 2.0.2 to 2.1.3

Important as 2.0.2 has a bug where it does not respect --min-size parameter.

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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • 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 <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@awgymer
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awgymer commented Mar 26, 2026

Tests are failing due to a significant bug I have identified in tjiangHIT/cuteSV#176.

The bug is actually unlikely to ever affect "real" data, but for our test data where there is a single chromosome but we give 2 threads, it can never succeed.

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