Move all rule to main Snakefile

[chrstphtrs]

No description provided.

[FabianHofmann]

We could even move rule all down to the other rules or?

[fneum]

You mean before rule purge? Yes. One would just have to check if snakemake -j8 would still trigger the all rule, or if it would go into one of the include: ... files

[coroa]

snakemake triggers the first rule by default, the name all is convention.
(first rule after inlining all the included files) EDIT: Indeed, included files are ignored: modularization docs.

[chrstphtrs]

Snakemake does not trigger rules from the include block. That was the reason we had to move the all rule outside of there in the first place. So yes, should move the all rule down to start off the block of other rules.