Snakemake wildcards from python wrapper not found

I am new to using snakemake and I am having difficulty. I have written a python wrapper file to run make snakefile. The wrapper takes a samples.txt with taxon, read1, read2, adapters, and assembly (Y/N). If assembly is needed, the snakefile with assembly is run, if N, a snakefile without assembly is run. It seems like the correct snakefile is being run, but the information for the wildcards isn't being transferred from the wrapper to the snakefile.

samples.txt

Solatube DRR350770_1.fastq.gz DRR350770_2.fastq.gz all.fa Y

run_pipeline.py

import argparse
import os

parser = argparse.ArgumentParser(description="Run Snakemake pipeline with Trinity assemble or not")
parser.add_argument("samples", help="path to samples.txt")
args = parser.parse_args()

with open(args.samples) as f:
    for line in f:
        taxon, read1, read2, adapters, assembly = [x.strip() for x in line.split()]
        if assembly == "Y":
            os.system(f"snakemake -s SNPwAssembly.smk --cores 16 --config taxon={taxon} read1={read1} read2={read2} adapters={adapters}")
        elif assembly == "N":
            os.system(f"snakemake -s SNPwoAssembly≈.smk --cores 16 --config taxon={taxon} read1={read1} read2={read2} adapters={adapters}")
        else:
            print(f"Invalid value for assembly in line: {line}")

SNPwAssembly.smk begins:

import os

# define rules                                                                                                                                                                                  
rule all:                                                                                                                                                                                               
    input: expand("{taxon}.snpden", taxon = taxon)                                                                                                                                                         
                                                                                                                                                                                                        
rule trinity_assembly:                                                                                                                                                                                  

input:                                                                                                                                                                                              
    read1 = "{taxon}/{read1}",                                                                                                                                                                      
    read2 = "{taxon}/{read2}",                                                                                                                                                                      
    adapters = "{adapters}"                                                                                                                                                                         
output:                                                                                                                                                                                             
    "{taxon}/trinity_out_dir/Trinity.fasta"                                                                                                                                                         
threads: 15                                                                                                                                                                                         
shell:                                                                                                                                                                                              
    '''                                                                                                                                                                                             
    singularity exec -e {trinity_path} Trinity --seqType fq --max_memory 450G --left SRR12102895_1.fastq.gz --right SRR12102895_2.fastq.gz --CPU 15 --trimmomatic --quality_trimming_params "all.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25" --output trinity_out_dir                                                                                                                                                                                         
    '''     

when I run python3 run_pipeline.py samples.txt, I get the error:

name 'taxon' is not defined

Minimum example:

For sample.txt, I would provide sample instead of reads.

Solatube DRR350770 all.fa Y

run_pipeline.py

import argparse
import os

parser = argparse.ArgumentParser(description="Run Snakemake pipeline with Trinity assemble or not")
parser.add_argument("samples", help="path to samples.txt")
args = parser.parse_args()

with open(args.samples) as f:
    for line in f:
        taxon, sample, adapters, assembly = [x.strip() for x in line.split()]
        if assembly == "Y":
            os.system(f"snakemake -s SNPwAssembly.smk --cores 16 --config taxon={taxon} sample={sample} adapters={adapters}")

For your SNPwAssembly.smk file:

TAXON = config['taxon']
SAMPLES = config['sample']
ADAPTERS = config['adapters']


print (TAXON)
print (SAMPLES)
print (ADAPTERS)

rule all:
    input:
        expand("{taxon}/{sample}_trinity/Trinity.fastq", taxon = TAXON, sample = SAMPLES)


rule test:
    input:
        read1 = "{taxon}/{sample}_1.fastq.gz",
        read2 = "{taxon}/{sample}_2.fastq.gz", 
    output:
        "{taxon}/{sample}_trinity/Trinity.fastq"
    params:
        adaptor = config['adapters']
    threads: 1
    shell:                                                                                                    
        """
        echo {input.read1} {input.read2} {params} {threads} > {output}
        """