Enable continuity i.e., End-to-End execution

[sreichl]

Goal: Once everything is done once i.e., every module was configured and executed, end-to-end execution should be possible for both, iterations with changed parameters and reproducibility.

• [ ] add how to use modules sequentially (also within recipes) If a module requires an annotation file generated by a previous rule, DAG construction fails if this file is missing. This can happen in project/recipe workflows where sequential module execution relies on outputs from preceding modules (e.g., an annotation file). The best practice is to run the workflow module by module, save the required output (e.g., the annotation file) externally, (e.g., to config/), and thereby making it re-runnable for future end-to-end execution for both, iterations with changed parameters and reproducibility. Checkpoints are no solution as they only apply to rules, not to modules loading data during DAG creation by Snakemake.
• [ ] https://github.com/epigen/dea_seurat/issues/16
• [ ] https://github.com/epigen/dea_limma/issues/12
• [ ] test (maybe unnecessary as implicit by recipes)

[sreichl]

add as an example the ATAC-seq or spilterlize_integrate scenario, where both modules create annotation files for downstream analyses inputs.