Snakemake perform rules based on configs

Question

I wish to do be able to write a workflow so that I can choose which optional rules to run in the config.json file. For example if I have a Snakefile with 2 rules, rule_a and rule_b, each with the same input but different outputs:

rule_a:
  input: input.txt
  output: out_a.txt
  run: ...

rule_b:
  input: input.txt
  output: out_b.txt
  run: ...

And I have the following configurations in the json file:

{
"run_a": "T",
"run_b": "F"
}

How do I write the Snakefile so that in this case only rule_a will be run while rule_b will be ignored?

Answer 1

As python can be used in snakemake scripts, you could use python code to identify which files need to be created.

Configfile config.json:

{
    "run_a": true,
    "run_b": false
}

Snakefile:

configfile: "config.json"

if config['run_a']:
    target = 'out_a.txt'
elif config['run_b']:
    target = 'out_b.txt'


rule all:
    input:
        target

rule a:
  input: 'input.txt'
  output: 'out_a.txt'
  shell:
    "touch {output}"

rule b:
  input: 'input.txt'
  output: 'out_b.txt'
  shell:
    "touch {output}"