Working on a template update nf core pipelines lint seems to nf-core #linting

Working on a template update. nf-core pipelines l...

Zachary Norgaard

09/17/2025, 8:38 PM

Working on a template update. nf-core pipelines lint seems to be ignoring my

.nf-core.yml

. Getting errors for ci pieces missing which are intentionally excluded from this nf-core style pipeline.

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files_exist: File not found: .github/workflows/nf-test.yml
files_exist: File not found: .github/actions/get-shards/action.yml
files_exist: File not found: .github/actions/nf-test/action.yml

My template block from

.nf-core.yml

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template:
  author: Zach Norgaard
  description: a bioinformatics pipeline that...
  force: false
  is_nfcore: false
  name: example_pipeline
  org: fulcrumgenomics
  outdir: .
  skip_features:
    - adaptivecard
    - changelog
    - ci
    - citations
    - codespaces
    - continuous_integration_testing
    - documentation
    - email
    - github
    - github_badges
    - gitpod
    - igenomes
    - license
    - nf_core_configs
    - rocrate
    - slackreport
    - vscode
  version: 1.0.0dev

I'd rather not edit the

files_exist

block directly. Any ideas on a

skip_feature

I'm missing?

mashehu

09/18/2025, 5:10 AM

Skip_feature is not skipping linting for it. You need to specify the linting rules to be ignored separately. See the linting docs for examples https://nf-co.re/docs/nf-core-tools/api_reference/3.3.2/pipeline_lint_tests/files_unchanged

Zachary Norgaard

09/18/2025, 3:21 PM

Hmm. I haven't been manually updating that section since it was autogenerated. Looks like it's a bit of a mess with duplicate entries. Good to know it's ok to clean that up!

Zachary Norgaard

09/18/2025, 3:26 PM

Now I'm more confused. In the linting section it should be checking for more things:

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lint:
  files_exist:
    - .editorconfig
    - .github/.dockstore.yml
    - .github/CONTRIBUTING.md
    - .github/ISSUE_TEMPLATE/bug_report.yml
    - .github/ISSUE_TEMPLATE/config.yml
    - .github/ISSUE_TEMPLATE/feature_request.yml
    - .github/PULL_REQUEST_TEMPLATE.md

And many of those don't exist either, but don't cause errors. I assumed that's because they were listed in the skip_features section. Seems like something is broken with linting in general or there are different skip strategies implemented in different ways.

Zachary Norgaard

09/18/2025, 3:48 PM

Nevermind. The documentation was a little confusing to me. These are the files we're skipping in the

file_exist

check.

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