Wildtype sequencing-based count error correction

[MaximilianStammnitz]

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[MaximilianStammnitz]

@BenjaminWehnert1008 here there'll be quite a few things still to discuss / edit:

1. How should the WT sequencing sample(s) be specified in the sample sheet .csv?
2. Should we run this seq error correction function (only takes a few seconds) as a loop over all samples in a single process, or rather as one process per sample?
3. Add this option to the nf-core input command (--wt_count_error_correction) and in that case there needs to be an extra check if the corresponding sequencing fastqs are actually specified in the sample sheet .csv
4. Need to generate the corresponding process / main.nf, potentially update config file(s), etc.
5. Need to adapt this R script so that the input path / output path / threshold parameter are correct
6. All the downstream tasks (e.g. heatmaps, fitness calculation, etc.) need to use variantCounts_filtered_by_library_err_corrected.csv instead of variantCounts_filtered_by_library.csv and variantCounts_for_heatmaps_err_corrected.csv instead of variantCounts_for_heatmaps.csv