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simplify logic for parsing of container configs#4277

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mashehu wants to merge 4 commits into
nf-core:devfrom
mashehu:simplify-container-config-parsing
Open

simplify logic for parsing of container configs#4277
mashehu wants to merge 4 commits into
nf-core:devfrom
mashehu:simplify-container-config-parsing

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@mashehu
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@mashehu mashehu commented May 11, 2026

Might be easier to review by commit.

The general rational:
No need to run nextflow inspect, if we anyway just check meta.yml in the end. Instead, parse a meta.yml for a specific module (update_container_config) or for all modules (generate_container_config) and build the container configs through there (getting the process name from the main.nf file on the way).

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codecov Bot commented May 11, 2026

Codecov Report

❌ Patch coverage is 91.86047% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.27%. Comparing base (b6af91a) to head (e472701).

Files with missing lines Patch % Lines
nf_core/pipelines/containers_utils.py 91.25% 7 Missing ⚠️

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@mashehu mashehu marked this pull request as ready for review May 11, 2026 13:22
@mashehu mashehu force-pushed the simplify-container-config-parsing branch from f34d28a to e472701 Compare May 11, 2026 13:35
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