Snakemake/Patterns

Snakemake patterns for Snakefiles and complex workflows.

creating a master rule

If Snakemake is not provided with a rule to execute, it will execute the first rule in the file.

To create a master rule that will call other rules defined in the Snakemake file, the make equivalent of "all" or "default", you should define it first (you can name it whatever you would like):

mynames   = ['A','B','C']
myinputs  = [j+".txt" for j in mynames]
myoutputs = [j+".dodat" for j in mynames]

rule default:
    input:
        myoutputs
    shell:
        'echo "i just run subrules!"'