nf-core / nf-core/tools

Re-test and label/exclude modules with failing tests

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#4,016 0 comments 0 reactions 1 assignee View on GitHub

@mashehu is already working on this.

Since Jan 30, 2026.

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Python
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Description

Problem

When a widely-used module (e.g., untar, samtools/index) is modified, it triggers tests for all dependent modules and subworkflows. This frequently surfaces pre-existing test failures in modules that haven't been tested in a while, blocking PRs that are unrelated to those failures.

This creates a frustrating situation where contributors end up debugging and fixing other people's broken tests just to get their own changes merged, or requiring maintainers to override CI failures.

Recent example: https://github.com/nf-core/modules/pull/9796 - a topic channel migration for 5 modules triggered failures in galah, kraken subworkflows, and others that were already broken.

Proposed Solution

As agreed in the nf-core maintainers meeting, implement a periodic CI job (weekly/monthly?) that:

  1. Runs all module/subworkflow tests regardless of changes
  2. Labels modules with failing tests (e.g., tests-failing, needs-fix)
  3. Optionally excludes known-failing modules from PR CI runs until fixed

This would:

  • Surface broken tests proactively rather than when someone touches a dependency
  • Make it clear which modules need attention
  • Prevent unrelated failures from blocking PRs
  • Provide a "health dashboard" for the modules repository

Additional Considerations

  • Labels could trigger notifications to module maintainers
  • A scheduled issue could be auto-created listing all failing modules
  • Consider a "quarantine" mechanism where known-failing tests are skipped in PR CI but tracked separately

Contributor guide

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First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Assessment

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