8000 limit get_wf_files to only consider files not ignored by git by mashehu · Pull Request #4593 · nf-core/tools · GitHub
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limit get_wf_files to only consider files not ignored by git - #4593

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mashehu wants to merge 1 commit into
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use-git-to-trim-down-workflow-file-search
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mashehu wants to merge 1 commit into
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use-git-to-trim-down-workflow-file-search

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@mashehu
@mashehu mashehu commented Nov 5, 2026
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codecov Bot commented Nov 5, 2026 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
â 8000 œ… Project coverage is 78.74%. Comparing base (0c7006d) to head (aa04daf).

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@mashehu
mashehu force-pushed the use-git-to-trim-down-workflow-file-search branch from f6b5adc to a790247 Compare November 5, 2026 10:41
@mashehu
mashehu force-pushed the use-git-to-trim-down-workflow-file-search branch from a790247 to aa04daf Compare November 5, 2026 20:46
@mashehu
mashehu requested a review from JulianFlesch November 6, 2026 09:28
@swastiktawate swastiktawate left a comment
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Smart fix, asking git itself which files are ignored is much more reliable than guessing with filename patterns. The test with a real git repo and nested ignore files is thorough. Two small things: the import subprocess sits inside the function rather than at the top of the file, is that on purpose? And the fallback only prunes folders when the pattern ends in *, so a pattern like *.log would not prune a folder. Is that covered anywhere?

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