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add pixi env#12165

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matthdsm wants to merge 4 commits into
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add/pixi
Open

add pixi env#12165
matthdsm wants to merge 4 commits into
masterfrom
add/pixi

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@matthdsm

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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.
  • 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

@matthdsm matthdsm requested review from a team as code owners June 25, 2026 11:42
Comment thread pixi.toml Outdated
@matthdsm

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Feel free to hit merge if there are no remaining issues

@mashehu mashehu left a comment

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maybe add docs on how to use this in the readme or contributing.md

@mashehu mashehu left a comment

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should we switch the devcontainer to also use this then, to keep them in sync?

@matthdsm

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Added an attempt, not sure if it'll work/ is correct

@mashehu

mashehu commented Jun 25, 2026

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cc @JulianFlesch can you have a look at the devcontainer please?

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3 participants