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Update GNU sort to comply to nf-core guidelines#11072

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mahesh-panchal merged 6 commits intonf-core:masterfrom
mahesh-panchal:fix/gnu-sort-ext-compliance
Mar 31, 2026
Merged

Update GNU sort to comply to nf-core guidelines#11072
mahesh-panchal merged 6 commits intonf-core:masterfrom
mahesh-panchal:fix/gnu-sort-ext-compliance

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@mahesh-panchal mahesh-panchal commented Mar 27, 2026

Description

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.
  • 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

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mahesh-panchal commented Mar 27, 2026

Why does this one pass? The gnu sort input is not updated


Reason: Nextflow <=25 only prints a WARN when tuple cardinality doesn't match. Using nextflow.enable.strict = true catches it.

@mahesh-panchal mahesh-panchal force-pushed the fix/gnu-sort-ext-compliance branch from d783cb4 to f4d5224 Compare March 30, 2026 08:46
@mahesh-panchal mahesh-panchal marked this pull request as ready for review March 30, 2026 09:00
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@mahesh-panchal mahesh-panchal added this pull request to the merge queue Mar 31, 2026
Merged via the queue into nf-core:master with commit 94e6aa4 Mar 31, 2026
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@mahesh-panchal mahesh-panchal deleted the fix/gnu-sort-ext-compliance branch March 31, 2026 18:12
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