Snakefile_bins

import os

configfile: "config_bins.yaml"

# SAMPLES = ["A", "B"]
# ASSEMBLIES = ["X","Y"]
# CENTRIFUGE_BASE = "/home/jgsanders/miniconda/envs/anvio2/centrifuge"

rule all:
    input:
        expand("data/bins/{assembly}/picked_bins.txt", assembly=config["ASSEMBLIES"])

rule pick_bins:
    input:
        bins_dir = "data/anvio/{assembly}/{assembly}_SAMPLES-SUMMARY-refined/bin_by_bin",
        bins_fp = "data/anvio/{assembly}/{assembly}_SAMPLES-SUMMARY-refined/general_bins_summary.txt",
        cov_fp = "data/anvio/{assembly}/{assembly}_SAMPLES-SUMMARY-refined/bins_across_samples/mean_coverage.txt"
    output:
        bins_outdir = "data/bins/{assembly}",
        bins_info = "data/bins/{assembly}/picked_bins.txt"
    params:
        A = config["A"],
        C = config["C"],
        R = config["R"],
        N = config["N"],
        sample = lambda wildcards: config["SAMPLES"][wildcards.assembly]
    script:
        "pick_bins.py"