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Merged
mashehu merged 9 commits into from
Nov 6, 2025
Merged

Add picrust2/pipeline module #9218

mashehu merged 9 commits into from
Nov 6, 2025

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@dialvarezs
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@dialvarezs dialvarezs commented Oct 21, 2025

Adds https://github.com/picrust/picrust2 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.
  • 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

SPPearce
SPPearce reviewed Oct 23, 2025
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@dialvarezs dialvarezs requested a review from SPPearce October 28, 2025 13:33
SPPearce
SPPearce approved these changes Oct 28, 2025
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SPPearce commented Oct 28, 2025

Good to go for me.

@dialvarezs
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dialvarezs commented Oct 28, 2025

Thanks @SPPearce!

@dialvarezs dialvarezs enabled auto-merge October 28, 2025 16:17
@dialvarezs dialvarezs disabled auto-merge October 28, 2025 16:17
@dialvarezs
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dialvarezs commented Oct 28, 2025

I guess that linting error won't let merging this the nice way :(

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SPPearce commented Oct 28, 2025

Yes, needs fixing

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SPPearce commented Oct 28, 2025

You need to adjust the meta to match your changes to the output channels

@dialvarezs
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dialvarezs commented Oct 28, 2025

It's a parsing bug in nf-core tools: nf-core/tools#3842

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SPPearce commented Oct 29, 2025

Oh, is it because you have the word "path"?

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dialvarezs commented Oct 29, 2025

Yes!

SPPearce
SPPearce reviewed Nov 6, 2025
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I guess there isn't a different name you could use?

@mashehu mashehu merged commit adc0bfd into nf-core:master Nov 6, 2025
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@dialvarezs @SPPearce @mashehu