Addition of a parameter for the minimum depth to call a base

[cjjossart]

Description of feature

Hello Viralrecon team,

I am requesting an addition of a parameter that would allow the user to supply a minimum depth to cal a base and thus variants as well. Currently this can be done by supplying a custom config with specific processes and update args to increase or lower the minimum depth. The variant calling and consensus modules would use this parameter. It would be ideal to have this as a parameter that can be set by a custom config or on the command line. I think the default of 10 works well, which is what these values are set in the config files. This would enhance the usability of this pipeline. Additionally, if possible it would ideal to have the metric table have a column for the genome fraction of the sample at the specified depth. For example, there is a column "% Coverage > 10x" that could possible be altered to reflect the minimum depth parameter being specified (i.e. '% Coverage > ${params.min_depth}x').

I wonder if the added parameter could be added and then placed in the config files, as to not alter or change the modules' code base. Please reach out with any questions or if I can provide further explanation. Thanks! -CJ