I have a snakemake rule where I call a python script with the script keyword: rule merge_results: input: [...] output: path_results script: "merge_results.py" However, I would like to also call an R script in this rule, depending on a condition. I wanted to do something like this: rule merge_results: input: [...] output: path_results script: "merge_results.py" if cond: "my_script.R" but Snakemake won't allow it. I know I could call my scripts by using the run and shell() keywords, but my python and R scripts use a lot of times the snakemake.input variable, so I would have to change a lot of things in their code in order to call them in a different way. Do you know if I can avoid that and use the script: keyword with multiples files ? Continue reading...