IKIM-Essen / uncovar

Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.

https://ikim-essen.github.io/uncovar

BSD 2-Clause "Simplified" License

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fix: changes in path requirements for snakedeploy #590

Closed AKBrueggemann closed 1 year ago

AKBrueggemann commented 1 year ago

Description

Changed the path fetching in common.smk -> get_resource(). Should fetch the total link if snake deploy is used so files can be used from the resources folder in the repository. ## Related Issue

Checklist

[x] I've formatted the PR title in accordance with the structure of the conventional commit messages.
[x] I've updated the code style using pre-commit if needed.
[x] I've updated or supplemented the documentation as needed.
[x] I've read the CODE_OF_CONDUCT.md document.
[x] I've read the CONTRIBUTING.md guide.

johanneskoester commented 1 year ago

The error is indeed a bug in Snakemake. Fix is here: https://github.com/snakemake/snakemake/pull/2170

johanneskoester commented 1 year ago

Thanks a lot @AKBrueggemann! Once the PR is merged and release, you can rerun the CI in this PR here, as it should automatically take the latest Snakemake.

AKBrueggemann commented 1 year ago

Thank you very much @johanneskoester!

johanneskoester commented 1 year ago

Needs another fix: https://github.com/snakemake/snakemake/pull/2179