Snakemake requires --cores (5.21.0)

[KasperThystrup]

With the current and earlier versions of snakemake, executing a pipeline without the --cores argument will yield an Error.
While users properly quickly becomes aware of this issue, it is something I think you might consider to address in the guide e.g. in 2 - Snakefiles - How do I set up default settings for snakemake and How do I write a simple workflow?

[sdruskat]

Just stumbled across this.

For this episode, I'd suggest adding -c 1 for each snakemake call, and explaining after the first snakemake? The alternative would be to introduce either a custom shell alias (too complicated IMHO), or introduce configfile right after the first call (with a potential error showing at the user's end)?

EDIT: It seems that cores aren't yet configurable via configfile...

[sdruskat]

Perhaps setting a temp variable may solve this, so only the instruction to set the variable needs to be added?

$> alias snakemake='snakemake -c1'