Issues

• Add single-line license header to all nf-core modules/subworkflows main.nf

  enhancement
  nf-core/tools#4510 · Filter by author jfy133 opened on Oct 9, 2026

• Allow nf-core modules container create to work for installed nf-core modules

  enhancement
  nf-core/tools#4508 · Filter by author awgymer opened on Oct 9, 2026

• Ignore the .pixi folder when linting and doing template merges

  bug
  nf-core/tools#4507 · Filter by author nvnieuwk opened on Oct 8, 2026
  4

• Default config interpolation error in pipeline lint

  bug
  nf-core/tools#4504 · Filter by author LouisLeNezet opened on Oct 8, 2026

• Software versions like 1.20 are turned into 1.2 when the versions YAML is parsed

  bug
  nf-core/tools#4500 · Filter by author piplus2 opened on Oct 7, 2026

• More informative error messages

  enhancement
  nf-core/tools#4498 · Filter by author ScottNortonPhD opened on Oct 7, 2026
  2

• Add --force and --all flags to modules/subworkflows patch command

  enhancement
  nf-core/tools#4494 · Filter by author ScottNortonPhD opened on Oct 2, 2026

• Typed pipelines and pipeline composition: lint and template changes

  nf-core/tools#4493 · Filter by author pinin4fjords opened on Oct 2, 2026

• pipelines lint crashes with a KeyError when a subworkflow imports a record type from a module

  nf-core/tools#4490 · Filter by author pinin4fjords opened on Oct 2, 2026

• 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
  4

• nf-core pipeline download fails with singularity

  awaiting-feedbackbug
  nf-core/tools#4484 · Filter by author remiolsen opened on Sep 30, 2026
  2

• 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

• 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
  4

• 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