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Include the centralized nf-core configs also in offline mode, if a local copy is available. #3491
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Include the centralized nf-core configs also in offline mode, if a local copy is available. #3491
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Does somebody have any pointers on the CI failures? During my manual tests, it seemed to work fine: pip3 install --upgrade --force-reinstall git+https://github.com/MatthiasZepper/tools.git@local_config_inclusion_when_offline |
It's due to the Nextflow edge version 😞 we have seen this on pipelines too. Nextflow team is working on a fix |
Ok, then we will wait. But otherwise, I think this is ready for review. |
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Looks good, thanks for addressing this!
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…n as a whole if no configs are to be included.
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: Fabian Egli <fabianegli@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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As discussed in #3430 it would be desirable to have the option to use the centralized configs also on offline HPCs, if they are available as a local copy. This PR implements this change as suggested by @bentsherman:
Rationale:
Additionally, it fixes the downstream issues that arose by this change:
nf-core pipelines lint
had to be significantly changed to accommodate to the fact that we now have multiple old versions of that code.nf_core/pipeline-template/.github/workflows/config_tests.yml
is a new GitHub Action to test, if a pipeline actually has the institutional configs available. It is run on pull requests tomain
, such that any issues should be caught prior to a pipeline release.nf-core pipelines create
was adapted so that the aforementioned GitHub Action is not included in a customized template when opting out of the centralized nf-core profiles.PR checklist
CHANGELOG.md
is updateddocs
is updated