How to use wildcards in input for snakemake rule

Question

I am having rel hard time understanding what I am doing in the following code. Could someone kindly help me with issue?

Partial Snakefile:

# load config file
configfile: "config.yaml"
import sys
import os

sample=config["Sample_Name"]
trainingset=config["trainingset"]
    
if config["batch_analysis"]:
    sample = []
    for name in os.listdir(config["base_dir"]):
        sample.append(name)
    sample.sort()
    input_dir = expand(config["base_dir"] + "/{sample}", sample=sample)
else:
    input_dir = config["FAST5_basedir"]
    
    out_dir = config["output_dir"]
    
    files_needed = ["modified_bases.5mC.bed", "basecalls.fastq", 
                    "mappings.sorted.bam", "mappings.sorted.bam.bai"]
    
rule all:
    input:
        expand("{out_dir}/{sample}/reports/{sample}_{trainingset}_WGS_report.pdf",
               out_dir=config["output_dir"], sample=sample, 
               trainingset=config["trainingset"])
    
rule megalodon:
    input:
        fast5_dir = input_dir,
        ref = config["ref_index"],
    output:
        touch(expand("{out_dir}/{sample}/megalodon/{files}",
                     files=files_needed, sample=sample, 
                     out_dir=config["output_dir"]))
    threads: 16
    conda:
        workflow.basedir + "/envs/megalodon.yaml"
    params:
        guppybasecallserver = config["megalodon_guppy_basecall_server"],
        guppy_params = config["megalodon_guppy_params"],
        additional = config["megalodon_additional_commands"],
        outputs = config["megalodon_outputs"],
        liveprocess = "--live-processing" if config["live_acquisition"] else "",
        overwrite = "--overwrite" if config["megalodon_overwrite"] else "",
    priority: 100
    shell:
        """
        megalodon '{input.fast5_dir}'
        --outputs {params.outputs}
        --reference {input.ref}
        --mod-motif m CG 0
        --devices 0
        --processes {threads}
        --sort-mappings
        --guppy-server-path {params.guppybasecallserver}
        --guppy-params "{params.guppy_params}"
        --output-directory "{out_dir}/{sample}/megalodon/"
        {params.liveprocess} {params.overwrite} {params.additional}
        """

Output from terminal: snakemake --snakefile megalodon_pipeline -c -n

[Tue Mar 29 22:40:17 2022] 
rule megalodon: 
    input: 
        /home/monib/MagDx/Testing_Folder/data/Test1, 
        /home/monib/MagDx/Testing_Folder/data/Test2, 
        /home/monib/MagDx/Testing_Folder/data/Test3, 
        /home/monib/MagDx/static/hg19.mmi  
    output:  
        /home/monib/MagDx_result/Test1/megalodon/modified_bases.5mC.bed,  
        /home/monib/MagDx_result/Test2/megalodon/modified_bases.5mC.bed,  
        /home/monib/MagDx_result/Test3/megalodon/modified_bases.5mC.bed,  
        /home/monib/MagDx_result/Test1/megalodon/basecalls.fastq, 
        /home/monib/MagDx_result/Test2/megalodon/basecalls.fastq,  
        /home/monib/MagDx_result/Test3/megalodon/basecalls.fastq,  
        /home/monib/MagDx_result/Test1/megalodon/mappings.sorted.bam,  
        /home/monib/MagDx_result/Test2/megalodon/mappings.sorted.bam,  
        /home/monib/MagDx_result/Test3/megalodon/mappings.sorted.bam,  
        /home/monib/MagDx_result/Test1/megalodon/mappings.sorted.bam.bai,  
        /home/monib/MagDx_result/Test2/megalodon/mappings.sorted.bam.bai,  
        /home/monib/MagDx_result/Test3/megalodon/mappings.sorted.bam.bai  
    jobid: 3  
    priority: 100  
    threads: 12  
    resources: tmpdir=/tmp 

The above rule does not iterate, instead the input is being used as concatenated string, instead of base_dir and sample being a wildcards.

Rest of the rules come up fine; it is just this rule I cannot get it to behave like a wildcard base_dir and sample in the input.