Dynamic Branching/Plumbling - snakemake

Question

Is it possible to use Dynamic Branching/Plumbing in a snakefile?
I wish to perform the following:
A -> B -> D
or
A -> C -> D
Depending on whether a config variable is true.
for example:
*(rules.B if config["deblur"] == True else rules.B),
In this instance it runs both rules B and C.
I have tried
if config["deblur"] == True:
rules.B,
else:
rules.C,
But this gives me a syntax error.
In the next rule the input is as follows.
input:
qiime_feature_table_input = rules.qiime_deblur.output.qiime_deblur_table if config["deblur"] == "True" else rules.qiime_denoise.output.qiime_denoise_table
Thanks for your help!

Answer 1

Since the value of the configuration variable is known before runtime, there's no need for dynamic modification of the DAG in this case. Here's a simple snakefile that will run rules a -> b -> d if config_var is true and rules a -> c -> d if config_var is false:
config_var = True
rule all:
input:
"d/out.txt",
rule a:
output:
"a/a.txt",
shell:
"""
echo 'a' > '{output}'
"""
rule b:
input:
rules.a.output,
output:
"b/b.txt",
shell:
"""
echo 'b' > '{output}'
"""
rule c:
input:
rules.a.output,
output:
"c/c.txt",
shell:
"""
echo 'c' > '{output}'
"""
rule d:
input:
rules.b.output if config_var else rules.c.output,
output:
"d/out.txt",
shell:
"""
cat '{input}' > '{output}'
"""

Answer 2

Not sure if this applies to your case, but one option could be to have these two rules produce the same file (it could be a dummy file), but define only one rule at a time with a conditional. Here's a rough pseudocode:
config_var = True
rule all:
input: 'test.txt'
if config_var:
rule B:
output: 'test.txt'
else:
rule C:
output: 'test.txt'