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CI for variant calling via Github Actions and CIEVaD #75
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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. |
add running --help for principal check after download
check thresholds for SNV and indel
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 |
.github/workflows/VariantCalling.yml
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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>
add shield to the README for indels and SNV F1-score for test status