Snakefile_paper_old

'''
This Snakemake contains the pipeline for the previous version of 
the paper. It can still be used with the previous version of
data on Zenodo (December 13, 2019).
'''

# Network Parameters
NETWORK=config["parameters"]["network_file"]
OUTPATH=config["parameters"]["outpath"]

GENESET=config["parameters"]["geneset_file"]
GENESET_CSV = config["parameters"]["geneset_csv"]
GENESET_NAME = config["parameters"]["tcga_dataset"]

TOPOLOGY = config["topology"]["analyse"]
ASSOCIATION = config["association"]["analyse"]
COMPARISON = config["within_comparison"]["analyse"]

EXTENSIONS=config['figures']['extension']
OUTFIGURES=config['figures']['outpath']




# If the matrices for the full analysis are not specified, they are generated by the rule
if len(config["parameters"]["sp_matrix"])>0:
    SP_MATRIX=config["parameters"]["sp_matrix"]
else:
    SP_MATRIX=OUTPATH+"_sp_matrix.hdf5"
if len(config["parameters"]["rwr_matrix"])>0:
    RWR_MATRIX=config["parameters"]["rwr_matrix"]
else:
    RWR_MATRIX=OUTPATH+"_rwr_matrix.hdf5"

include: "rules/paper_analysis.smk"
include: "rules/paper_visualise.smk"
include: "rules/paper_hdn.smk"
include: "rules/paper_sbm.smk"


rule download_data:
    input:
        expand(OUTPATH+"datasets/{n}/"+GENESET_CSV, n=GENESET_NAME)

rule all:
    input:
        expand(OUTPATH+"table_topology_{t}.csv", t=TOPOLOGY),
        expand(OUTFIGURES+"barplot_{t}.{e}", t=TOPOLOGY, e=EXTENSIONS),
        expand(OUTPATH+"table_association_{t}.csv", t=ASSOCIATION),
        expand(OUTFIGURES+"heatmap_association_{t}.{e}", t=ASSOCIATION, e=EXTENSIONS),
        expand(OUTPATH+"table_within_comparison_{t}.csv", t=COMPARISON),
        expand(OUTFIGURES+"heatmap_within_comparison_{t}.{e}", t=COMPARISON, e=EXTENSIONS),

rule single_all:
    input:
        expand(OUTPATH+"table_topology_{t}.csv", t=TOPOLOGY),
        expand(OUTFIGURES+"barplot_{t}.{e}", t=TOPOLOGY, e=EXTENSIONS),
        expand(OUTPATH+"table_association_{t}.csv", t=ASSOCIATION),
        expand(OUTFIGURES+"volcano_{t}.{e}", t=ASSOCIATION, e=EXTENSIONS),
        OUTPATH+"table_diffusion.csv"

rule multi_all:
    input:
        expand(OUTPATH+"table_topology_{t}.csv", t=TOPOLOGY),
        expand(OUTFIGURES+"barplot_{t}.{e}", t=TOPOLOGY, e=EXTENSIONS),
        expand(OUTPATH+"table_within_comparison_{t}.csv", t=COMPARISON),
        expand(OUTFIGURES+"heatmap_within_comparison_{t}.{e}", t=COMPARISON,e=EXTENSIONS),

rule hdn_all:
    input:
        OUTPATH+"final_hdn.csv"

rule sbm_all:
    input:
        OUTPATH+"final_sbm.csv"