I would like to be able to have my snakemake workflows continue running even when certain rules fail.
For example, I'm using a variety of tools in order to perform peak-calling of ChIP-seq data. However, certain programs issue an error when they are not able to identify peaks. I would prefer to create an empty output file in such cases, and not having snakemake fail (like some peak-callers already do).
Is there a snakemake-like way of handling such cases, using the "shell" and "run" keywords?
Thanks