Integrating Relative Amplicon Coverage

[gordonkoehn]

This PR attempts to integrate the following script into this installable package such that it may, in the future, be easily integrated into V-Pipe.

Amplicon Coverage Test

Integrating this into V-Pipe will allow others using the pipeline to profit from this quality check.

This PRs main objective was to:

• implement a Snakemake workflow for per batch generation of coverage_heatmaps

further this PR improved code quality by:

• replace argparse with click
• reformated to black and ruff standards
• adds some typing and explanatory comments

Considerations:

• consider using click instead of argparse (Ivan)
• Make one Snakemake rule per batch (Ivan / Matteo)
• Remove Unused Plotting functions for a clean code base - confirmed with Matteo

Open Questions:

• Some of the plotting functions originally commented out are - I left commented out. Are they needed? make_median_cov_hist, make_median_coverage_barplot, ...

[gordonkoehn]

I can currently run and reproduce the plots. Given the test_data from Matteo.

[gordonkoehn]

The script works per batch now. :) With Snakemake Rules per Batch :) Some clean up still pending.

[gordonkoehn]

NB: I activated all commented-out plots. This may not be needed.

• check with Matteo / David