Snakemake

#snakemake (Private) is something I should definitively look into https://snakemake.github.io/

https://slides.com/johanneskoester/snakemake-tutorial

Here is another one https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/

https://github.com/leipzig/SandwichesWithSnakemake

I am having an issue to deal with a singlae archive beeing expanded to multipl folder

here is maybe a way https://taylorreiter.github.io/2020-02-03-How-to-use-snakemake-checkpoints-to-extract-files-from-an-archive/

So apparently two mechanisms can be used

checkpoints and dynamics

http://ivory.idyll.org/blog/2021-snakemake-checkpoints.html

https://evodify.com/snakemake-checkpoint-tutorial/