8000 Msisensorpro: updated tool to v1.3.0 by Tuur-ds · Pull Request #8532 · nf-core/modules · GitHub
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Msisensorpro: updated tool to v1.3.0 #8532

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Merged
merged 9 commits into from
May 22, 2025
Merged

Msisensorpro: updated tool to v1.3.0 #8532

merged 9 commits into from
May 22, 2025
+36 −56

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Tuur-ds
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@Tuur-ds Tuur-ds commented May 21, 2025

PR checklist

Closes #XXX

  • 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.
  • Emit the versions.yml file.
  • 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

@Tuur-ds Tuur-ds changed the title Msisensorpro/scan: updated tool to v1.3.0 Msisensorpro: updated tool to v1.3.0 May 22, 2025
@nvnieuwk
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@maxulysse and @LouisLeNezet seems like this update doesn't have the germline and somatic outputs. Is this an issue for Sarek?

maxulysse
maxulysse reviewed May 22, 2025
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@maxulysse maxulysse left a comment

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Why removing these outputs?

@Tuur-ds
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Tuur-ds commented May 22, 2025

When running the test these 2 files are not generated in this version of the tool, i will add them back and mark them as optional for now

nvnieuwk
nvnieuwk approved these changes May 22, 2025
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Sounds like a good solution for now :)

@Tuur-ds Tuur-ds added this pull request to the merge queue May 22, 2025
Merged via the queue into nf-core:master with commit 4557423 May 22, 2025
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@Tuur-ds Tuur-ds deleted the msisensorpro/scan branch May 22, 2025 12:59
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