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CI for variant calling via Github Actions and CIEVaD #75

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merged 48 commits into from
Jun 12, 2024

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Krannich479
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@Krannich479 Krannich479 commented May 16, 2024

  • test CovPipe's variant calling via CIEVaD
  • add shield to the README for indels and SNV F1-score for test status

@Krannich479 Krannich479 added the enhancement New feature or request label May 16, 2024
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Please suspend the PR at least for the time of CIEVaD being a private repo. We'd need to update tokens in rki-mf1/covpipe2 to make the checks work but this becomes obsolete once the repo goes public.

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In future versions of this Variant Calling test I might add caching such that the benchmark scores are read dynamically from previous runs. At the moment they are static integers. However, for the caching the test needs to be merged into the original CovPipe2 repository first. Plus, I am not certain yet whether this (complexity of system engineering) reduces the understanding of how to use CIEVaD's results. tbd

@Krannich479 Krannich479 self-assigned this May 29, 2024
@Krannich479 Krannich479 requested a review from MarieLataretu May 29, 2024 15:24
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Would it make sense to upload result files from CIEVaD as artifacts? 🤔

I saw it at the lining CI at nf-core:
https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/.github/workflows/linting.yml#L60-L68

and I have it here to check results, when the test failed:
https://github.com/rki-mf1/CoVpipe2/blob/main/.github/workflows/pytest_workflows.yml#L58-L68

Co-authored-by: MarieLataretu <52002068+MarieLataretu@users.noreply.github.com>
@Krannich479 Krannich479 merged commit 4459fed into rki-mf1:main Jun 12, 2024
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