CODEWITHSUNDEEP
parameterschainingsnakemake
tedtoal
tedtoal

Reputation: 1080

chained parameters in SnakeMake

This appears to work in SnakeMake to chain parameters. Is this okay to do, or is it going to cause problems in parallel environment, and should a PersistentDict be used instead?

rule a:
    params:
            a = "Param A", b="Param B"
    ...


rule b:
    params: rules.a.params.b

Upvotes: 0

Views: 82

Answers (1)

TBoyarski
TBoyarski

Reputation: 441

I would advise against that approach as it results in a needlessly coupled system

E.g Now "rule b" must ALWAYS be accompanied by "rule a"

I say needlessly because another option is to declare external variables in a YAML (or JSON) file and have both param directives accept it as an argument.

config.yaml ~ Personal Example

a: Param A
b: Param B

Snakefile ~ Personal Example with just a single rule

configfile: "config.yaml"

rule a:
    ...
    params:
        importantRuleAVar = config["a"]
    ....


rule b:
    ...
    params:
        importantRuleBVar = config["a"]
    ...

This is critical in my pipeline as I need the same wildcard_constraint regex for large parts of my pipeline, yet I didn't want to end up coupling all the rules together.

Also good for things like quality thresholds on aligners. Sometimes you'll use similar thresholds in different aligners for comparative purposes.

Upvotes: 2

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