chore: use `--cores all` in snakemake CI test, format .sh script

[corneliusroemer]

If testing locally, we have more than 1 core available, so why not make use of it.

For CI it shouldn't change anything since the runners only have 1 core.

[j23414]

[non-blocking comment]

I see we're changing "runner.sh", not sure if we want to make it --cores all for all the snakemake calls:

• https://github.com/search?q=org%3Anextstrain+%22snakemake%22+%22--cores+1%22&type=code

[victorlin]

@j23414 that's a good point, I think this is scoped to Augur only so just need to update tests/builds/add_to_alignment/Snakefile according to https://github.com/nextstrain/augur/search?q=snakemake+cores+-extension%3Amd&type=Code

[corneliusroemer]

We should probably now merge master into this so that the tests pass, right? @victorlin

[victorlin]

We should probably now merge master into this so that the tests pass, right? @victorlin

Update to latest yes, but the "proper" way by historical convention here would be to git rebase -i master and force-push for a cleaner history.