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Command to generate pipeline container config files #3955

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@mirpedrol mirpedrol commented Dec 2, 2025 •
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close #3953

Done:

  • New function to run nextflow inspect and obtain docker config file
  • New function to (re)generate all container config files
  • Container config files are regenerated with nf-core modules install|update|remove

TODO:

  • Add tests
  • Test a lot
  • What happens if the module is not found?
    • Modules form multiple repos
    • Modules included as an alias
  • Is there a case where two modules have the same name but different container? how to solve this?
  • Could the code be used to reduced duplication with download command?

@mirpedrol mirpedrol force-pushed the pipeline-container-config-builder branch from 6341cd3 to b8004aa Compare December 2, 2025 14:43
mashehu
mashehu reviewed Dec 3, 2025
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mashehu
mashehu reviewed Dec 3, 2025
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mirpedrol and others added 3 commits December 4, 2025 14:59
@mirpedrol
always update docker amd64
0954ee6
@mirpedrol @mashehu
Update nf_core/pipelines/containers_utils.py
f5502c9 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@mirpedrol
spaces
7d2586d
@mirpedrol mirpedrol marked this pull request as ready for review December 4, 2025 14:39
mashehu
mashehu reviewed Dec 4, 2025
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mirpedrol and others added 2 commits December 15, 2025 15:04
@mirpedrol @mashehu
Apply suggestions from code review
0ab8425 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@mashehu
Merge branch 'dev' into pipeline-container-config-builder
66ef73b
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codecov bot commented Dec 15, 2025 •
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Codecov Report

❌ Patch coverage is 97.18310% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.76%. Comparing base (a70e6f2) to head (c3d04f0).

Files with missing lines Patch % Lines
nf_core/pipelines/containers_utils.py 96.55% 2 Missing ⚠️

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@mirpedrol mirpedrol changed the title [WIP] Command to generate pipeline container config files Command to generate pipeline container config files Dec 16, 2025
mashehu
mashehu approved these changes Dec 16, 2025
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@mashehu mashehu mentioned this pull request Dec 16, 2025
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