ENH: Reduce number of required CLI parameters for interactive/exploratory use

[corneliusroemer]

Currently, this is our simplest example for how to use Nextclade in our docs:

nextclade \
   --input-fasta data/sars-cov-2/sequences.fasta \
   --input-dataset data/sars-cov-2 \
   --output-tsv output/nextclade.tsv \
   --output-tree output/nextclade.auspice.json \
   --output-dir output/ \
   --output-basename nextclade

Many if not most of these parameters are required. It would be nice for quick exploratory use if the output options defaulted to sensible values. If I just want to quickly run a few sequences through Nextclade, I want all the output enabled and don't care exactly what the files are named and in which folder it's placed.

If users want and/or need to specify, they always can, but I don't see why we shouldn't have defaults. That would make it much easier to quickly run nextclade without having to consult the documentation.

Despite having used Nextclade extensively, I still don't know off by heart which parameters are necessary and what their names are. However, the following I would be able to remember:

nextclade -i in.fa -d data/sars-cov-2

The output parameters from above could default to the values given above, or maybe --output-dir nextclade-output for reduced conflict probability.