Implementing Base Count Coverage Depth

[gordonkoehn]

This Pull Request (PR) aims to integrate quality control scripts from @AugusteRi in this new package usefulGnom.

Aplogies, this PR is messy and includes some unrelated project setup.

All three scripts can now be run as snakemake rules flexible to location, enddate of samples:

1. calculating basecnt coverage depth,
2. total coverage depth and
3. computing frequency matrix+calculating mutations statistics

I`ve verified the outputs against the original scripts on Euler.

For the full analysis for Zürich with the last samples from the 07_03 the workflows directory one can now simply run:

snakemake -c 2 mutation_statistics_Zürich_2024_07_03

or for individual output files.

snakemake -c 2         ${OUTDIR}Zürich (ZH)/lineplotC23039G_G22599C_Zürich (ZH)_2024-07-03.pdf"
snakemake -c 2         ${OUTDIR}Zürich (ZH)/heatmapC23039G_G22599C_Zürich (ZH)_2024-07-03.pdf"

To configure this script, you need to edit the paths in workflows/base_coverage. stick for your personal Euler setup and the location of data files.

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Open Questions:

@AugusteRi I hope I integrated the script as it's intended to be run. I stuck as closely to your setup as I understood it, this leaves ad-hoc filters you had in your code not integrated as of now.

• Do we need to integrate protocoll as another filter?
• Do we need to take care of the startdate ?

More generally,

• Are these typical .tsv formats and datafiles ? I've assumed so, and integrated the reading and parsing into usefulGnom for future scripts.

[gordonkoehn]

Yes, Script 1: basecnt_coverage runs as a snakemake rule basecnt_coverage_depth

[gordonkoehn]

Second script added no errors

[gordonkoehn]

NB: these scripts are mostly reading/ parsing/ matching - not much core logic to write tests for easily. Hence there are no tests.

[gordonkoehn]

Minor Open Questions to @AugusteRi

[gordonkoehn]

@AugusteRi Do we need to integrate the protocol as another filter? Is this an argument that should be crucial to pass down? You didn't integrate it in the file naming before, so I excluded it for now.

[gordonkoehn]

@AugusteRi Do you typically change the start date? Is it worth adding this as another parameter to the final command? I assume the start date is rarely changed, as you did before, so I also excluded it from the final command.