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Update nf-core modules#853

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dialvarezs merged 12 commits intonf-core:devfrom
dialvarezs:update-modules
Aug 22, 2025
Merged

Update nf-core modules#853
dialvarezs merged 12 commits intonf-core:devfrom
dialvarezs:update-modules

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@dialvarezs dialvarezs commented Aug 22, 2025 •
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I updated a big bunch of nf-core modules here.
Most of them are just meta.yml updates, and a few version bumps.
One notable update is BUSCO to v6.0.0 that should solve #838.

There's still some modules to update:

─ [!] 14 Module Test Warnings ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                       ╷                                           ╷                                                                           │
│ Module name                           │ File path                                 │ Test message                                                              │
│╶──────────────────────────────────────┼───────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────╴│
│ adapterremoval                        │ modules/nf-core/adapterremoval            │ New version available                                                     │
│ bcftools/consensus                    │ modules/nf-core/bcftools/consensus        │ New version available                                                     │
│ bcftools/index                        │ modules/nf-core/bcftools/index            │ New version available                                                     │
│ bcftools/view                         │ modules/nf-core/bcftools/view             │ New version available                                                     │
│ dastool/dastool                       │ modules/nf-core/dastool/dastool           │ New version available                                                     │
│ dastool/fastatocontig2bin             │ modules/nf-core/dastool/fastatocontig2bin │ New version available                                                     │
│ fastp                                 │ modules/nf-core/fastp                     │ New version available                                                     │
│ freebayes                             │ modules/nf-core/freebayes                 │ New version available                                                     │
│ genomad/download                      │ modules/nf-core/genomad/download          │ New version available                                                     │
│ genomad/endtoend                      │ modules/nf-core/genomad/endtoend          │ New version available                                                     │
│ gtdbtk/classifywf                     │ modules/nf-core/gtdbtk/classifywf         │ New version available                                                     │
│ multiqc                               │ modules/nf-core/multiqc                   │ New version available                                                     │
│ porechop/abi                          │ modules/nf-core/porechop/abi              │ New version available                                                     │
│ porechop/porechop                     │ modules/nf-core/porechop/porechop         │ New version available                                                     │
│                                       ╵                                           ╵                                                                           │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

But they have some bigger changes in the code, so they could need updates in the subworkflows or at least a more testing. I'll leave them for another PR, so you can have a cleaner review 😅.

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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@dialvarezs dialvarezs linked an issue Aug 22, 2025 that may be closed by this pull request
Busco local variable 'target_id' referenced before assignment #838
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@dialvarezs dialvarezs marked this pull request as ready for review August 22, 2025 15:28
@dialvarezs dialvarezs changed the title Update modules Update nf-core modules Aug 22, 2025
prototaxites
prototaxites approved these changes Aug 22, 2025
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Thanks @dialvarezs!

@dialvarezs dialvarezs merged commit d0c1533 into nf-core:dev Aug 22, 2025
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@dialvarezs dialvarezs deleted the update-modules branch August 22, 2025 19:09
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@prototaxites prototaxites prototaxites approved these changes

@jfy133 jfy133 Awaiting requested review from jfy133 jfy133 is a code owner

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

@muabnezor muabnezor Awaiting requested review from muabnezor muabnezor is a code owner

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Busco local variable 'target_id' referenced before assignment

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