Allow default `platform` and `scheme_name` values on command line

[rambaut]

Description of feature

Allow an option to specify the platform (illumina or ont) and the scheme_name for all samples when these columns are missing from the sample-sheet. This would simplify the sample-sheet when being used through GUIs like Epi2ME as these options can be selected in the UI from dropdown menus. The minimum sample-sheet would then be barcode and sample id.

[BioWilko]

Hi Andrew

This would add significant complexity to samplesheet validation and could lead to a lot of nasty downstream impacts, would this sort of thing not be best inside a samplesheet builder? Be that a nxf pipe or a GUI app of some sort?

[ammaraziz]

One option to simplify the validation is to have --platform and --scheme_name override the samplesheet input. This might work well for downstream modules that are species specific. For example, nextclade can only run with --platform and --scheme_name are specified and not through samplesheet.

This is all extra complexity though...