Snakemake Pipeline Issue

[AzlanNI]

Hello together i am using Snakemake to create a tool with my different bash and python scripts. I am really new to Snakemake so i guess i am doing something wrong here. THis is my Skript

input_csv = os.getenv("INPUT_CSV")
output_dir = os.getenv("OUTPUT_DIR")
Motif_list = os.getenv("MOTIF_LIST")
data = pd.read_csv(input_csv)

input_base = os.path.splitext(os.path.basename(input_csv))[0]
updated_csv = os.path.join(output_dir, f"{input_base}_updated.csv")

bed_files = expand(os.path.join(output_dir, "{file_name}.bed"), file_name=data['File_name'].tolist())

rule all:
    input:
        updated_csv,
        bed_files

rule run_python_script:
    input:
        input_csv
    output:
        updated_csv
    shell:
        """
        python /Users/azlannisar/Desktop/Skripts/Check_python_snaky.py {input} {output}
        """

rule run_modkit:
    conda:
        "/Users/azlannisar/Snakemake_project_Mikrob/environment.yaml"
    input:
        csv_file=updated_csv
    output:
        os.path.join(output_dir, "{file_name}.bed")
    params:
        reference_path=lambda wildcards: data[data['File_name'] == wildcards.file_name].iloc[0]['Reference_path'],
        pod5_path=lambda wildcards: data[data['File_name'] == wildcards.file_name].iloc[0]['pod5_path']
    shell:
        """
        modkit pileup {params.pod5_path}/*_sorted.bam {output} --ref {params.reference_path}
        """

rule run_5mC_analysis_script:
    input:
        csv_list="/Users/azlannisar/Snakemake_Test/Data_Test2_updated.csv",
        motif_list="/Users/azlannisar/Motifs_5mC.txt"
    params:
        output_dir="/Users/azlannisar/Snakemake_Test"
    conda:
        "/Users/azlannisar/Snakemake_project_Mikrob/analysis.yaml"
    shell:
        """
        python /Users/azlannisar/Desktop/Skripts/analysis_5mC_script.py {input.csv_list} {params.output_dir} {input.motif_list}
        """

When i run this is runs the first two rules without problems gives me no Error and Skips the last rule. So i am confused why it is doing that. Since if i copy the last rule out into a seperate file and run is there it creates the outputs without problems. Maybe someone with more snakemake experience can help me out. Thanks and kind regards!
Azlan

[cmeesters]

Your last rule has no output directive. Nor is it picked by all.

[AzlanNI]

@cmeesters Thanks for ur answer i got it running for a while forgot to close the ticket sry!