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New module savana/cna#11926

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manascripts wants to merge 3 commits into
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manascripts:savana-cna
Open

New module savana/cna#11926
manascripts wants to merge 3 commits into
nf-core:masterfrom
manascripts:savana-cna

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@manascripts

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This PR adds a new module savana/cna.
Because it requires an adequately large test dataset for copy number fitting @cortés‑ciriano‑lab/savana#110, only a stub test is included.

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

@SPPearce

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I really don't like the stub only test here.
Is there anything in the sarscov2 data that could be used? https://github.com/nf-core/test-datasets/tree/modules/data/genomics/sarscov2/nanopore/bam

@manascripts

manascripts commented Jun 12, 2026

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@SPPearce, as @helrick mentioned here - the 2 MB bam would be too small for the copy number fitting. Plus, there are issues running the tool using a single contig fasta. I have used this tool as a local module in the past and it worked alright with a full-fledged dataset. Do you have any suggestions for this case?

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