satijalab / azimuth-meta-analysis Goto Github PK

Hello,
first of all, thanks for providing this repo! I'm just getting started working on some of the lung datasets that have been processed by you, so this is a very useful resource to get started in this new field.

I've cloned the repo and tried to run the snakemake workflow as described in the readme, however, I ran into the following issue:

snakemake --use-singularity --cores 2 RULE
Building DAG of jobs...
MissingRuleException:
No rule to produce RULE (if you use input functions make sure that they don't raise unexpected exceptions).

Would you be able to help me with this?

Best wishes,
Anika

Hi,

when running snakemake --use-singularity download
Building DAG of jobs...
WorkflowError:
Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards at the command line, or have a rule without wildcards at the very top of your workflow (e.g. the typical "rule all" which just collects all results you want to generate in the end).

how can this be fixed.

Thank you

best regards
Monib