How to run one part of a Snakemake pipeline without rerunning entire pipeline?

I am trying to test that one section of the pipeline produces the correct output.

I am running Snakemake by submitting a bash script to a cluster, and have tried adding:
--rule
--allowed-rules

inside of a for loop so that the entire command is: run_pipeline.sh <rule1> <rule2> etc...

When I use --rule, it says that the rules cannot contain wildcards.
When I use --allowed-rules, it says nothing to be done, files already present.

The --allowed-rules message is not accurate because the correct output files are not generated.

Do I really have to rerun the entire pipeline and delete all previous input files or is there a better way?

Instead of using internal commands like --allowed-rules (for which the documentation states: "Note that this is intended primarily for internal use and may lead to unexpected results otherwise.") use one of the following:

> --until, -U <target>
>
> Runs the pipeline until it reaches the specified rules or files. Only runs jobs that are dependencies of the specified rule or files, does not run sibling DAGs.
>
> --omit-from, -O <target>
>
> Prevent the execution or creation of the given rules or files as well as any rules or files that are downstream of these targets in the DAG. Also runs jobs in sibling DAGs that are independent of the rules or files specified here.

If you are unsure what the targets are, it can help to visualise your DAG.

Your pipeline should not rerun all rules, but only those of files affected by your changes to the pipeline or files affected by rules with --force exeucion.