Issues

• test_full CI overwrites plugin scope defined in the pipeline causing failures

  bug
  nf-core/tools#4487 · Filter by author FriederikeHanssen opened on Oct 1, 2026
  3

• nf-core pipeline download fails with singularity

  bug
  nf-core/tools#4484 · Filter by author remiolsen opened on Sep 30, 2026
  1

• nf_core.utils.fetch_wf_config json cache files for nextflow config output don't differentiate between old -flat and new -o json config formats

  bug
  nf-core/tools#4481 · Filter by author jmuhlich opened on Sep 28, 2026

• linting error on multiqc

  bug
  nf-core/tools#4479 · Filter by author LilyAnderssonLee opened on Sep 22, 2026

• Lint: warn when a docs page will not be rendered on the website

  nf-core/tools#4474 · Filter by author erikrikarddaniel opened on Sep 19, 2026
  

• Reduce privileged-token exposure in fix_linting.yml

  nf-core/tools#4471 · Filter by author pinin4fjords opened on Sep 16, 2026
  1

• nf-core/tools: EDAM ontology map covers 61 of 728 format concepts, and a failed download is indistinguishable from "no term exists"

  nf-core/tools#4468 · Filter by author TilakSharma07 opened on Sep 11, 2026

• Malformed or missing manifest.name gives opaque error / IndexError instead of a lint failure

  bug
  nf-core/tools#4467 · Filter by author fpmartinez10 opened on Sep 10, 2026
  1

• API reference pages are not available

  bug
  nf-core/tools#4465 · Filter by author OlivierCoen opened on Sep 4, 2026

• IndexError: string index out of range

  bug
  nf-core/tools#4464 · Filter by author OlivierCoen opened on Sep 4, 2026

• missing build_id value

  awaiting-feedbackbug
  Bug

  nf-core/tools#4458 · Filter by author maxulysse opened on Aug 31, 2026
  2

• Missing corresponding arm build

  nf-core/tools#4457 · Filter by author maxulysse opened on Aug 31, 2026

• Add support to Apple container

  enhancement
  nf-core/tools#4456 · Filter by author mribeirodantas opened on Aug 26, 2026
  

• Formatting issues when generating container definitions

  bug
  nf-core/tools#4452 · Filter by author matthdsm opened on Aug 21, 2026

• nf-core pipelines lint silently suppresses all module linting on error.

  bug
  nf-core/tools#4447 · Filter by author awgymer opened on Aug 19, 2026
  4

  

• Action Required: Fix Renovate Configuration

  nf-core/tools#4446 · Filter by author renovate opened on Aug 18, 2026
  2

  

• Add linting to flag outdir being set in test_full or test

  enhancement
  nf-core/tools#4440 · Filter by author FriederikeHanssen opened on Aug 6, 2026
  1

• [request] Lint for a potential runtime error with nf-test and github actions

  enhancement
  nf-core/tools#4419 · Filter by author heylf opened on Jul 28, 2026

• Lint error: KeyError: 'manifest.name' with contributor ORCiD

  bug
  nf-core/tools#4416 · Filter by author nickp60 opened on Jul 23, 2026
  1

• --plain-text for test commands

  enhancement
  nf-core/tools#4372 · Filter by author itrujnara opened on Jul 3, 2026
  

• Pull online test-datasets with nf-core pipelines download

  downloadenhancement
  Enhancement

  nf-core/tools#4370 · Filter by author JosuaCarl opened on Jul 2, 2026

• Ro-crate path to file not being automatically updated

  bug
  nf-core/tools#4369 · Filter by author JoseEspinosa opened on Jul 2, 2026

• Schema validation parses string incorrectly if they're quoted integers

  bug
  nf-core/tools#4367 · Filter by author CormacKinsella opened on Jul 1, 2026

• Linting or GHA to test whether all modules of a module suite are updated

  enhancementlintingmodules
  nf-core/tools#4355 · Filter by author famosab opened on Jun 26, 2026 · 4.2.0
  1

• Auto-updated markdown table of default resource requests in pipeline template

  enhancement
  nf-core/tools#4345 · Filter by author jfy133 opened on Jun 24, 2026
  6