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: include flag fix #451

Closed AKBrueggemann closed 2 years ago

AKBrueggemann commented 2 years ago

Description

The workflow still had a problem concerning the include flag. The output from get_assemblies_for_submission is a path, not a name, leading to a KeyError in get_include_flag in the common.smk. This way, all sequences are included in the report, also the ones with an initial include flag of 0. ## Related Issue

Checklist

thomasbtf commented 2 years ago

I'll wait for #447 for the review. It is not very obvious what was changed.