Loss of certain values when using dict and expand together in Snakemake

I have try to use a function to return a dict as a rule input, here is a simple expamle:

# debug.smk
input_a='/{output}/to/{group_name}/input_a'
input_b='/{output}/to/{group_name}/input_b'

rule_a=True
rule_b=True

output='output'
group_name='group_name'

def get_rule_output(): 
    output={}
    if rule_a: 
        output['output_a']=expand(input_a, output=output, group_name=group_name)
        print(expand(input_a, output=output, group_name=group_name))
    if rule_b: 
        output['output_xx']=expand(input_b, output=output, group_name=group_name)

    print(output)
    
    return output

rule all: 
    input: 
        get_rule_output(), 

I use following command to run it

snakemake -s debug.smk

My expected:

get_rule_output() return a dict with two output

{'output_a': ['/output_a/to/group_name/input_a'], 'output_xx': ['/output_a/to/group_name/input_b']}

however, its return value is

{'output_a': [], 'output_xx': ['/output_a/to/group_name/input_b']}

debug output by print() is following

snakemake -s snakemake/debug.smk
['/output_a/to/group_name/input_a']
{'output_a': [], 'output_xx': ['/output_a/to/group_name/input_b']}
Building DAG of jobs...

#other snakemake debug output

The choice of variable names is unfortunate. There are two variables output, one is used for the output and another one is defined in the workflow as:

output='output'

This leads to circularity in variable expansion. Fixing the names should resolve the issue.

You need to rename output={} inside your function:

In your code output has two meanings:

• output='output' which is also the value you want to use in expand(...)
• output={} which is the dictionary you want to hold your results, but which you are using in your expand(...) instead

Due to the local scope, output={} is used instead of output='output' for your expand(...) statement.

This works

# debug.smk
input_a = "/{output}/to/{group_name}/input_a"
input_b = "/{output}/to/{group_name}/input_b"

rule_a = True
rule_b = True

output = "output"
group_name = "group_name"


def get_rule_output():

    d= {}

    d["output_a"] = expand(input_a, output=output, group_name=group_name)
    d["output_b"] = expand(input_b, output=output, group_name=group_name)

    print(d)

    return output


rule all:
    input:
        get_rule_output(),