# Boilerplate Snakemake for Genomics Data Processing
configfile: "configs/config.yaml"

rule all:
    input:
        "results/tables/normalized_counts.csv"

rule quality_control:
    input:
        "data/raw/{sample}.fastq.gz"
    output:
        "data/processed/qc/{sample}_fastqc.html"
    conda:
        "envs/qc.yaml"
    shell:
        "fastqc {input} -o data/processed/qc/"

rule normalize_data:
    # A placeholder for your specific R/Limma or Scanpy logic
    input:
        expand("data/processed/qc/{sample}_fastqc.html", sample=config["samples"])
    output:
        "results/tables/normalized_counts.csv"
    script:
        "src/scripts/normalize.py"