Split a repository using Snakefile

[lucaz88]

Hi,

It would be interesting to have the possibility to split a Snakemake repository using a Snakefile/s.

I started to develop my workflow following the guidelines of "Distribution and Reproducibility" (https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html) to organize the repository folder. However, over time, the workflow has branched and, because those "daughter"-workflows were sharing some rules, envs, scripts, ..., I did not split them into different directories.

I see now that this was probably not the best choice but back then the idea was to avoid redundancies and the need to propagate the updates.

I've opened a similar ticket on Stack Overflow (https://stackoverflow.com/questions/78155378/how-to-copy-all-files-rules-envs-called-by-a-snakefile-into-a-new-reposito) without much luck so far.