nf-core / nf-core/tools

Lint for custom meta fields introduced into modules

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#2,537 1 comment 0 reactions 0 assignees View on GitHub

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enhancement
Dominant language
Python
Stars
322
Forks
255
Avg merge
2d 3h
Merged PRs (30d)
5

Description

Description of feature

The guidelines say that to keep modules generally applicable, no custom meta fields should be used, but passed as parameters.
A few have managed to sneak in.

It would be nice to have a lint check that doesn't allow anything other than:

  • meta.method(), e.g. meta.subMap()
  • meta.id
  • meta.single_end
  • meta.strandedness

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  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.

Research direction

Start by locating the existing lint checks in the Python tools package and identify where module metadata fields are parsed or validated. Confirm how the checker distinguishes the listed allowed accesses from other custom meta fields, then add coverage showing that only those forms pass and other custom fields fail.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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