nf-core / nf-core/tools

Add linting to flag outdir being set in test_full or test

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

Description

Description of feature

Some pipelines set outdir in their test_full config to a local results path. This is not flagged on the full-size tests, because we explicitly overwrite it. However, it can trip up users when they run the pipelines on their system. Since outdir is already defined the parameter validation does not catch it. Depending on the system they will only notice it, when the pipeline has completed and the results folder is missing.

It would be great to have a linting option that checks that outdir is not defined in any of the test configs.

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First steps

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  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 linting entry point and the tests covering pipeline test configurations. Trace how test and test_full configs are inspected, then add coverage showing that an outdir defined in either config is reported; done means the linting option flags these definitions without affecting full-size test behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
65/100

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