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Add new module: octopusv/plotcircos#12374

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manascripts wants to merge 3 commits into
nf-core:masterfrom
manascripts:octopusv-plot-circos
Open

Add new module: octopusv/plotcircos#12374
manascripts wants to merge 3 commits into
nf-core:masterfrom
manascripts:octopusv-plot-circos

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This PR adds octopusv/plotcircos module.

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

Comment thread modules/nf-core/octopusv/plotcircos/main.nf Outdated
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.circos.get(0).get(1)),

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why not the whole output including meta?
what about the second output. A tsv should be not too unstable (or you use https://github.com/lukfor/nft-csv to capture some characteristics)

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With the test data, the file would be empty

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then i would at least capture the file name.

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Okay, will update

manascripts and others added 2 commits July 15, 2026 15:50
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Comment on lines +31 to +32
file(process.out.circos.get(0).get(1)),
process.out.findAll { key, val -> key.startsWith('versions') }

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Suggested change
file(process.out.circos.get(0).get(1)),
process.out.findAll { key, val -> key.startsWith('versions') }
sanitizeOutput(process.out, unstableKeys: ["oversized_intra"])

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2 participants