Thanks. Haven't had the time to try it out but will do soon. I think having a single snakefile would be easier in many cases, but in my case it would be way too long. I have never used targets so will look up exactly what they are and how to use them. Will probably make understanding your code easier. --- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/kyleam/snakemake-mode/issues/12#issuecomment-212501913