Re: https://ecoevo.social/@ryneches/109714977686786493

1-snakemake-combinatorics.md

Run as

snakemake all_c

and you'll get this:

$ tree
.
├── a
│   ├── orange
│   ├── red
│   └── yellow
├── b
│   ├── blue
│   ├── green
│   └── purple
├── c
│   ├── orange-blue
│   ├── orange-green
│   ├── orange-purple
│   ├── red-blue
│   ├── red-green
│   ├── red-purple
│   ├── yellow-blue
│   ├── yellow-green
│   └── yellow-purple
└── Snakefile

3 directories, 16 files

Snakefile

rule a:
    output: "a/{a}"
    shell: """
        echo {wildcards.a:q} > {output:q}
    """

rule b:
    output: "b/{b}"
    shell: """
        echo {wildcards.b:q} > {output:q}
    """

rule c:
    input:
        a="a/{a}",
        b="b/{b}"
    output: "c/{a}-{b}"
    shell: """
        cat {input.a:q} {input.b:q} > {output:q}
    """

rule all_c:
    input: expand("c/{a}-{b}", a=["red", "orange", "yellow"], b=["green", "blue", "purple"])