Hello and Happy New Year to everyone!
I am a novice snakemake/programming user and I am still trying to figure some things out. So bare with me!
I am trying to make a pipeline with various steps that run different programs. In each step I would like to give the option to the user to choose which program to use.
In my mind I have it like this:
Snakemake --cores 10 --assembly metaspades --binning metabat --trimming trimmomatic
I would like the user to choose which software to run at each step. Is that possible or I am talking nonsense?And if yes, how can I do this?
Thanking you in advance!