An example of parameterizing snakemake workflows with a simple CLI.

Usage:

./run <workflow_file> <parameters_file>

e.g.

rm -f hello.txt
./run workflow-hello params-amy

creates hello.txt with "hello amy" in it, while

rm -f hello.txt
./run workflow-hello params-beth

creates hello.txt with "hello beth" in it.

Here, the workflow file workflow-hello.json specifes the target hello.txt , while the parameters file params-amy parameterizes the workflow with the name "amy".

Likewise,

rm -f goodbye.txt
./run workflow-goodbye params-beth

will put goodbye beth in goodbye.txt .

All workflows use the same set of Snakemake rules in Snakefile .

See also: https://github.com/charlesreid1/2019-snakemake-cli