snakemake target rule as variable for python code

I have a snakemake workflow that does a lot of work before it reaches the definition of the rules (querying files, accessing databases, filtering a data frame). Not all of this work is necessary, depending on the target rule I want to invoke.

How can I know which target rule is selected on the command line? Then I could have the pure-python work done upfront be limited to only what is necessary for that target rule.

Desired example, for which I need to know if the "snakemake.target_rule" variable exists and which variable it actually is:

def do_work_for_target_a():
    lots_of_work()
    return table

def do_work_for_target_b():
    lots_of_work()
    return table

if snakemake.target_rule == 'a':
   table_a = do_work_for_target_a()
elif snakemake.target_rule === 'b':
   table_b = do_work_for_target_b()
else:
   table_a = do_work_for_target_a()
   table_b = do_work_for_target_b()

rule all:
   input:
       "output_a.txt",
       "output_b.txt",

rule a:
   input:
       "output_a.txt",


rule b:
   input:
       "output_b.txt",

This is not a direct answer to your question, but a workaround that achieves the same result. The main idea is to create a temporary file whose only purpose is to run the rule-specific preparations:

def do_work_for_target_a():
    lots_of_work()

def do_work_for_target_b():
    lots_of_work()

rule all:
   input:
       "output_a.txt",
       "output_b.txt",

rule pre_a:
   output: temp("pre_a.txt")
   run:
      do_work_for_target_a()

rule pre_b:
   output: temp("pre_b.txt")
   run:
      do_work_for_target_b()


rule a:
   input:
       "pre_a.txt",
       "output_a.txt",

rule b:
   input:
       "pre_b.txt",
       "output_b.txt",

> How can I know which target rule is selected on the command line

A quite crude solution could be to parse the sys.argv list and determine the target rule. I'm not sure how to implement this robustly though.

I don't know of any intended way to access the name of the target rule name(s) from the CLI inside the Snakefile either.

As a workaround I suggest passing an additional --config value with the snakemake call, e.g. snakemake --config prep_for=<a|b> -- <remainder of your snakemake call> and make the modifications to your Snakefile to access that config value:

def do_work_for_target_a():
    lots_of_work()
    return table

def do_work_for_target_b():
    lots_of_work()
    return table

if config.prep_for == 'a':
   table_a = do_work_for_target_a()
elif config.prep_for === 'b':
   table_b = do_work_for_target_b()
else:
   table_a = do_work_for_target_a()
   table_b = do_work_for_target_b()

...