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