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refactor: parameterise optitype module and update to 1.5.0 - #12641

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nf-core:masterfrom
SpikyClip:update_optitype
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refactor: parameterise optitype module and update to 1.5.0#12641
SpikyClip wants to merge 3 commits into
nf-core:masterfrom
SpikyClip:update_optitype

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@SpikyClip

@SpikyClip SpikyClip commented Aug 9, 2026

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  • Refactors optitype module by adding named parameters
  • Updates optitype to version 1.5.0
  • Adds cplex package to container for completeness so that all three optitype solvers are supported
  • Enable multithreading for cbc/cplex solvers

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!
  • 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

…0, add cplex into env to support all solvers.
@SpikyClip
SpikyClip requested a review from jonasscheid August 9, 2026 23:53
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