workflow/preprocess.smk

rule preprocess:
    params:
        max_iter = config.get('max_iterations', 3)
    input:
        [
            "{BASE_DIR}/solution/arrays/signal_raw.npy",
            "{BASE_DIR}/solution/arrays/data_raw.npy"
        ]
    output:
        [
            "{BASE_DIR}/arrays/bkgd.npy",
            "{BASE_DIR}/arrays/signal.npy"
        ]
    shell:
        "python supervisor_coder.py --prompt preprocess --out_dir {BASE_DIR} --config {CONFIG} --input-files {input} --output-files {output} --max_iterations {params.max_iter}"