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At the moment, creating a PoN without data on chromosome X is bound to fail due to a bug in
ichorCNA (GavinHaLab/ichorCNA#26).

It is unclear when a new version will be out, so I have patched the current bioconda package
(bioconda/bioconda-recipes#61045) and built new container images, which I want to update to in this PR.

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

At the moment, creating a PoN without data on chromosome X is bound to
fail due to a bug in
ichorCNA(GavinHaLab/ichorCNA#26).

It is unclear when a new version will be out, so I have patched the
current bioconda package
(bioconda/bioconda-recipes#61045) and built
new container images, which I want to update to in this PR.
@lbeltrame
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I can't seem to run the tests locally (missing plugin): am I right in stating that the difference is in the versions.yml checksums?

@SPPearce
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SPPearce commented Dec 9, 2025

Yes, looks like they are failing due to the versions.yml having changed.

@lbeltrame
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Hopefully I did everything right(TM) and they should pass now. I'll update the branch once I make sure they do.

@lbeltrame lbeltrame self-assigned this Dec 9, 2025
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Ok, all tests pass now.

@lbeltrame lbeltrame added this pull request to the merge queue Dec 10, 2025
Merged via the queue into nf-core:master with commit a507bfc Dec 10, 2025
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@lbeltrame lbeltrame deleted the update-ichorcna-build branch December 10, 2025 06:46
vagkaratzas pushed a commit that referenced this pull request Dec 12, 2025
…9531)

* Bump ichorCNA package build in ichorcna/createpon and ichorcna/run

At the moment, creating a PoN without data on chromosome X is bound to
fail due to a bug in
ichorCNA(GavinHaLab/ichorCNA#26).

It is unclear when a new version will be out, so I have patched the
current bioconda package
(bioconda/bioconda-recipes#61045) and built
new container images, which I want to update to in this PR.

* Update some md5sums

* Update test snapshot

* Update test snapshot
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2 participants