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linting: capture correct error for invalid .nf-core.yml#4080

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mashehu merged 6 commits intonf-core:devfrom
mashehu:fix-load-tools-config-error
Apr 1, 2026
Merged

linting: capture correct error for invalid .nf-core.yml#4080
mashehu merged 6 commits intonf-core:devfrom
mashehu:fix-load-tools-config-error

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@mashehu mashehu commented Mar 4, 2026

Closes #3573

New error output (e.g. for scnanoseq) is

ERROR    Config file '.nf-core.yml' is invalid
         lint.pipeline_todos: Input should be a valid boolean
         Got instead: ['README.md', 'main.nf']

@mashehu mashehu requested a review from mirpedrol March 4, 2026 14:42
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codecov Bot commented Mar 4, 2026 •
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Codecov Report

❌ Patch coverage is 0% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 78.45%. Comparing base (7feb0a2) to head (450004e).
⚠️ Report is 2 commits behind head on dev.

Files with missing lines Patch % Lines
nf_core/commands_modules.py 0.00% 1 Missing ⚠️

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@mashehu mashehu force-pushed the fix-load-tools-config-error branch from fc2d1ed to 7943d8d Compare March 5, 2026 09:19
@mashehu mashehu force-pushed the fix-load-tools-config-error branch from 7943d8d to 0088e00 Compare March 6, 2026 10:59
@mashehu mashehu added this to the 4.0.0 milestone Mar 31, 2026
@mashehu mashehu merged commit 92500c9 into nf-core:dev Apr 1, 2026
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@JulianFlesch JulianFlesch JulianFlesch approved these changes

@mirpedrol mirpedrol Awaiting requested review from mirpedrol

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