nf-core / nf-core/tools

Add a way to tell the linter to ignore specified directories

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#3,385 2 comments 0 reactions 0 assignees View on GitHub

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

Description

Description of feature

Is there a way to configure the linter to ignore certain files/directories? As part of how our pipeline works, it creates very large caches of downloaded data to be reused. These typically end up in the source directory during testing. Linter checks like the one that looks for unhanded merge conflicts never finish on these 500Gb+ folders. I have to move these directories out manually to run the linting and then move them back in for testing.

@ewels suggested this could be implemented by ignoring any files in .gitignore. I imagine this would work well in most cases, at least as a good default.

Contributor guide

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First steps

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Research direction

The issue does not name a file or test. Start by locating the linter entry point and the check for unhandled merge conflicts, then trace how directories are traversed. Done means a configured or .gitignore-based directory is skipped and large ignored folders no longer delay linting; add coverage for that behavior if the project has linter tests.

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
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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