Snakefile_mediation

# This is the Snakefile for mediation analysis.

phenos=open("input/phenos_n209.txt").read().splitlines()
diets=["1D", "2D", "20", "40"]

rule all:
    input:
        expand("output/{diet}/{pheno}.Rds", diet=diets, pheno=phenos)

rule mediation:
    input:
        mb="../results/kraken_genus_clr_filt_w_comm_n107x2997_231017.txt",
        # mb="../results/DO_pathway_log2tpm_filt_w_comm_n273x2997.txt",
        pheno="../results/phenotype_values_closest_to_each_stool_ID_within_100_days_n2915x210_230811.txt",
        stool_meta="../data/metadata/stool_metadata_after_QC_no_controls_n2997_240418.txt",
        mouse_meta="../data/metadata/AnimalData_Processed_20230712.csv"
    output:
        "output/{diet}/{pheno}.Rds"
    log:
        "logs/{diet}_{pheno}.log"
    params:
        diet="{diet}",
        pheno="{pheno}"
    resources:
        mem_mb=32768
    threads: 32 
    envmodules:
        "R/4.0.2"
    script:
        "run_mediation_one_diet_one_pheno.R"