Add default profile to set Snakemake CLI args

[corneliusroemer]

The special profile at profiles/default/config.yaml is used by snakemake >= 7.29 by default without requiring passing in via --profile profiles/default

Profiles are nice because they reduce number of CLI args required when invoking snakemake, e.g. one no longer needs to use --cores 1 or -c1 which became necessary in snakemake at some point.

With the default profile, one can simply run the tutorial by typing snakemake.

[joverlee521]

This prompted me to read more about Snakemake profiles. Good to know that the default profile can be unset with --profile=none if you don't have another profile to provide.

[genehack]

The PR overall looks good to me, but I wonder if this should be cores: 1 to better reflect how the current tutorial instructions tell people to run things?

[victorlin]

I would think to not introduce the additional complexity of profiles here - we don't use use them for most pathogen repos.

If the goal is to remove the unnecessary --cores argument, we can already remove that - it's not required as of Nextstrain CLI 4.0.0.

[genehack]

This PR seems to have become Warnocked — can we either determine what changes are required to allow it to be merged, or close it out?

[tsibley]

I vote to close for the reasons Victor gave.