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Test pipelines with Singularity & Conda #3098

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mirpedrol opened this issue Aug 5, 2024 · 1 comment
Open

Test pipelines with Singularity & Conda #3098

mirpedrol opened this issue Aug 5, 2024 · 1 comment
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@mirpedrol
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Description of feature

Pipelines are only tested with Docker. We should add tests with Singularity and Conda too.
Test with Singularity and Conda only on PRs to master + workflow dispatch. To avoid running the tests too often.
Linting: Singularity should be required, but Conda must be optional (opt-out) for pipelines which use custom Docker containers.

@edmundmiller
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Kinda a seperate issue but thought it might be a good place for the discussion.

I was thinking about this in terms of nf-core/modules.

Since we use the merge_queue, what if we only ran singularity and conda when the merge_queue is ran? It seems like the conda environment creation in some modules takes a really long time to get created(and in nf-test it creates the environment every time).

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