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Merged
merged 8 commits into from
Oct 25, 2024
Merged

Download: Seqera container support - Patch 1 #3244

merged 8 commits into from
Oct 25, 2024

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@MatthiasZepper
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@MatthiasZepper MatthiasZepper commented Oct 23, 2024 •
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This PR extends the tests so that Seqera Container support is tested for. It also tweaks the symlink function to support the unconventional registry that Seqera Containers uses.

This is a basic patch. It does neither add oras:// support nor does it fix the issue with the container priority resolution (#3179). For modules using Seqera containers, nf-core download will always download both containers, the native Singularity one and convert the Docker container to Singularity as well.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@MatthiasZepper MatthiasZepper changed the base branch from seqera_containers_example to dev October 24, 2024 17:17
@MatthiasZepper MatthiasZepper changed the title Addition to Seqera containers example Download: Seqera container support - Patch 1 Oct 24, 2024
@MatthiasZepper MatthiasZepper added the download nf-core download label Oct 24, 2024
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codecov bot commented Oct 24, 2024 •
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Codecov Report

Attention: Patch coverage is 80.00000% with 4 lines in your changes missing coverage. Please review.

Project coverage is 75.34%. Comparing base (354311d) to head (32a7e6b).
Report is 17 commits behind head on dev.

Files with missing lines Patch % Lines
nf_core/pipelines/download.py 80.00% 4 Missing ⚠️
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mashehu
mashehu approved these changes Oct 25, 2024
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pinin4fjords
pinin4fjords approved these changes Oct 25, 2024
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Thank you for this resolution, we appreciate you :-)

@MatthiasZepper @mashehu
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32a7e6b 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@MatthiasZepper MatthiasZepper merged commit 65db460 into nf-core:dev Oct 25, 2024
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@MatthiasZepper MatthiasZepper deleted the seqera_containers_example_mod branch October 25, 2024 13:17
@pinin4fjords pinin4fjords mentioned this pull request Oct 25, 2024
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@MatthiasZepper MatthiasZepper mentioned this pull request Nov 22, 2024
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@MatthiasZepper MatthiasZepper mentioned this pull request Jul 14, 2025
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

@mashehu mashehu mashehu approved these changes

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Seqera Containers
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