feat: benchmarking with other workflows

[thomasbtf]

Description

This PR includes benchmarking rules to compare the following workflows:

• ARTIC fieldbioinformatics
• ncov2019-artic-nf
• nf-core/viralrecon
• poreCov
• CoVpipe
• HaVoc
• Signal
• SnakeLines
• V-pipe
• UnCoVar

The benchmark consisted of

• a precision/recall analysis of the variant call files,
• an execution time overview,
• lineage call comparison based on pangolin, and finally
• a sequence analysis based on quast metrics of the consensus sequences.

To get the above-mentioned analysis run:

snakemake --cores all --use-conda --snakefile benchmarking/Snakefile  --resources nextflow=1 signal=1 vpipe=1 snakeline=1 uncovar=1

The plots can then be found under results/benchmarking/plots.

It can happen that the hard disk space is not sufficient. Here it helps to delete the "work" folder of nextflow manually to free up a few GB.

See notion for further steps.

Related Issue

N/A

Checklist

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• [X] I've updated the code style using pre-commit if needed.
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• [X] I've read the CODE_OF_CONDUCT.md document.
• [X] I've read the CONTRIBUTING.md guide.