Lint should not require specification of cores

[corneliusroemer]

Is your feature request related to a problem? Please describe.
I would like not to have to type -c1 when running the linter. The linter should work without specification of the number of cores, just like dryrun doesn't require number of cores.

❯ snakemake lint
Error: you need to specify the maximum number of CPU cores to be used at the same time. If you want to use N cores, say --cores N or -cN. For all cores on your system (be sure that this is appropriate) use --cores all. For no parallelization use --cores 1 or -c1.

Snakemake version: 6.5.2

[corneliusroemer]

The same problem occurs with snakemake --cleanup-metadata.

In fact, the command that is suggested does not run, because one needs to add the cores as -c1 for example. So either the docs should be changed or the behaviour of the command:

(nextstrain) [roemer0001@worker01 ncov-simple]$ snakemake --profile=profiles/basel-combined-cluster deploy_test all -npr -t
Building DAG of jobs...
IncompleteFilesException:
The files below seem to be incomplete. If you are sure that certain files are not incomplete, mark them as complete with    snakemake --cleanup-metadata <filenames>

To re-generate the files rerun your command with the --rerun-incomplete flag.Incomplete files:pre-processed/gisaid/alignment.fasta.xz

(nextstrain) [roemer0001@worker01 ncov-simple]$ snakemake --cleanup-metadata pre-processed/gisaid/*
Error: you need to specify the maximum number of CPU cores to be used at the same time. If you want to use N cores, say --cores N or -cN. For all cores on your system (be sure that this is appropriate) use --cores all. For no parallelization use --cores 1 or -c1.

(nextstrain) [roemer0001@worker01 ncov-simple]$ snakemake --cleanup-metadata pre-processed/gisaid/* -c1(nextstrain)

[HenningTimm]

This seems to have been fixed. In case of --lint, I think the call would have to be snakemake --lint, since without the dashes lint is interpreted as a target rule. The lint parameter is already in the list of parameters that do not require execution (and thus require a number of cores). For --cleanup_metadata this was added in #1429.

[corneliusroemer]

Thank you for clarifying @HenningTimm!