I need to integrate as inputs/outputs scripts written in python, R as well as shell scripts. I also would like to add to this list jupyter notebooks in constructing modular pipelines. While I found in the documentation about snakemake that some of this is possible, I did not find a clear indication as of the use of shell scripts inside the snakemake code. I also found that snake make integrates shell commands.
My questions are: Can snakemake integrate shell scripts in building bioinformatics pipelines? Can nextflow integrate it and other scripts (and jupyter notebooks) as well?
I have no experience in using snakemake or nextflow but willing to do so in future.