How to tell snakefmt to ignore a line in a Snakefile?

I have written a Snakefile “prepare_tuples.smk” having prepare_tuples as my head rule.
The input is defined as the output of the rule hadd_tuples.
When I run snakemake prepare_tuples -F -c20 I get the following error message:

I have an analysis pipeline that I want to run many times with different config files and I do not want to be able to infer the differences between the different configs from the file path as this will become extremely long (in the real example I will iterate over many different variables).

I am using a snakemake post deploy script to install additional software and check for requirements. The script contains following lines

I am not getting why snakemake is not able to identify the dependencies in this simple example. I am expecting that it identify that the input of main is generated in simulation and the inputs of the last one in setup. However, it looks like it is not the case. Th idea of this “rule architecture” is to parallelise at simulation level.