Thomas Battenfeld

SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly

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Hello V-pipe Team, I am from the University Hospital Essen, Germany, and we work extensively with SARS-CoV-2 in our research. We have also developed a [SARS-CoV-2 workflow](https://github.com/IKIM-Essen/uncovar). In preparation for...

## Feature Request Add csv table in report of all kallisto calls ## Motivation Needed for ww. ## Alternatives Maximum likelihood? ## Additional context N/A

## Version - UnCoVar version: 0.15.0 - Snakemake version: 7.3 ## Bug Report ## Minimal Example ## Logs ## Additional context

## Feature Request Resources essential for the workflow must be placed under `workflow/resources`. Access to these files must be done with `workflow.source_path("../resources/some-resource.txt")`. ## Motivation Snakedeploy doesn't work with v0.14.0 ##...

## Feature Request From @folker in #446: > we might want to add a few more illumina sequences to the CI environment ## Motivation ? ## Alternatives N/A ## Additional...

## Feature Request Add a minimum percentage of SARS-CoV-2 in the sample as criteria to create a pseudo assembly. ## Motivation It is confusing to have a pseudo assembly if...

Add variant overview plot

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## Feature Request Add a plot that contains the following: - The ORFS / genes of the SARS-CoV-2 Genome. See Example [1] below. - The protein products of the SARS-CoV-2...

e.g. `turbo` for sequential data. See https://vega.github.io/vega/docs/schemes/ and https://altair-viz.github.io/user_guide/customization.html#customizing-colors for more info.

Complete Documentation

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## Feature Request We have documentation of the workflow now 🎉 See. https://ikim-essen.github.io/uncovar/ But it's still empty 😔 @alethomas, @AKBrueggemann, @lenakinzel and everyone else: Please feel free to lent and...