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Download: Seqera container support - Patch 1 #3244

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MatthiasZepper
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@MatthiasZepper MatthiasZepper commented Oct 23, 2024

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

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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Thank you for this resolution, we appreciate you :-)

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@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
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3 participants