SIEVE_benchmark_pipeline/efficiency_benchmark.snake at main · szczurek-lab/SIEVE_benchmark_pipeline · GitHub

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"""
Run all tools locally.

Explanation of wildcards:

dataType: input data types, e.g., no CNVs, including CNVs, excluding CNVs, etc.
datasetName: simulated dataset names, e.g., 0001, 0002, 0003...
fineTuneTypeSieve: types of fine-tuning to perform for SIEVE defined in the configuration file, e.g., single thread, multi thread, etc.
fineTuneTypeCellPhy: types of fine-tuning to perform for CellPhy defined in the configuration file, e.g., single thread, multi thread, etc.
runTemplateStage1: configuration templates for SIEVE which will be the
first stage of the two-stage strategy.
runTemplateStage2: configuration templates for SIEVE which will be the
second stage of the two-stage strategy.
"""


configfile: "config.yaml"
include: "scripts/constants.py"
include: "scripts/utils.py"


#########################################################
#                Generate simulated data                #
#########################################################

generate_simulated_data(
    SIMUDATAROOT,
    config["tools"]["SIEVE_simulator"],
    config["configFiles"]["SIEVE_simulator"],
    SIMUDATAROOT + "simulation.log",
    config["benchmark"]["simulation"]["dataDir"],
    config["fineTune"]["SIEVE_simulator"]["overwrite"],
    SIMUMONOVARDIR + config["benchmark"]["simulation"]["bamFileNamesWithNormal"],
    SIMUMONOVARDIR + config["benchmark"]["simulation"]["bamFileNamesWithoutNormal"],
    SIMUSCIPHIDIR + config["benchmark"]["simulation"]["bamFileNamesWithNormal"],
    SIMUSCIPHIDIR + config["benchmark"]["simulation"]["bamFileNamesWithoutNormal"]
)


########################################################
#          Include predefined snakemake files          #
########################################################

include: "simulated_data.snake"
include: "monovar.snake"
include: "sciphi.snake"
include: "cellphy.snake"
include: "sieve_2stage.snake"
include: "sifit_local.snake"


#########################################################
#              Get categories of wildcards              #
#########################################################

SIMUDATASETNAMES = get_dataset_names(SIMUSNVSITESDIR)
FINETUNETYPESSIEVE = get_fine_tune_types(
    config["fineTune"]["beast"],
    config["benchmark"]["fineTuneTypes"]
)
FINETUNETYPESCELLPHY = get_fine_tune_types(
    config["fineTune"]["cellphy"],
    config["benchmark"]["fineTuneTypes"]
)
SIMUDATATYPES = get_data_types(
    config["benchmark"]["simulatedDataTypes"],
    config["benchmark"]["simulation"]["dataTypes"]["CNVTypes"]
)


#########################################################
#        Get paramemter estimates type for SIEVE        #
#########################################################

PARAMSESTIMATETYPE = get_parameter_estimate_type(config["fineTune"]["variantCaller"]["estimates"])


########################################################
#        Get the working directory of SNAKEMAKE        #
########################################################

SNAKEMAKEDIR = get_abs_working_dir()


#########################################################
#                       All rules                       #
#########################################################

rule all:
    input:
        expand(MONOVARTRUEPARAMSDIR + "{dataType}/{datasetName}/monovar.vcf", dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),

        expand(SCIPHIDIR + "{dataType}/{datasetName}/" + config["benchmark"]["simulation"]["sciphiFilePre"] + ".vcf", dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),
        expand(SCIPHIDIR + "{dataType}/{datasetName}/" + config["benchmark"]["simulation"]["sciphiFilePre"] + ".params.txt", dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),
        expand(SCIPHIDIR + "{dataType}/{datasetName}/" + config["benchmark"]["simulation"]["sciphiFilePre"] + ".probs", dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),
        expand(SCIPHIDIR + "{dataType}/{datasetName}/" + config["benchmark"]["simulation"]["sciphiFilePre"] + "/best_index/tree.gv", dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),

        expand(SIEVEFROMCANDIDATEVARCALSTAGE2DIR + "{fineTuneTypeSieve}/{dataType}/{runTemplateStage1}-{runTemplateStage2}/{datasetName}/sieve.estimates", fineTuneTypeSieve=FINETUNETYPESSIEVE, dataType=SIMUDATATYPES, runTemplateStage1=config["configFiles"]["sieve"]["stage1FileNames"], runTemplateStage2=config["configFiles"]["sieve"]["stage2FileNames"], datasetName=SIMUDATASETNAMES),
        expand(SIEVEFROMCANDIDATEVARCALSTAGE2DIR + "{fineTuneTypeSieve}/{dataType}/{runTemplateStage1}-{runTemplateStage2}/{datasetName}/stage2_files", fineTuneTypeSieve=FINETUNETYPESSIEVE, dataType=SIMUDATATYPES, runTemplateStage1=config["configFiles"]["sieve"]["stage1FileNames"], runTemplateStage2=config["configFiles"]["sieve"]["stage2FileNames"], datasetName=SIMUDATASETNAMES),

        expand(CELLPHYTRUEMONOVARSNVSDIR + "{fineTuneTypeCellPhy}/{dataType}/{datasetName}/vcf_ep/{datasetName}.raxml.bestTree", fineTuneTypeCellPhy=FINETUNETYPESCELLPHY, dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),
        expand(CELLPHYTRUEMONOVARSNVSDIR + "{fineTuneTypeCellPhy}/{dataType}/{datasetName}/vcf_ep/{datasetName}.raxml.bestModel", fineTuneTypeCellPhy=FINETUNETYPESCELLPHY, dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),

        expand(SIFITTRUEMONOVARSNVSTRUEPARAMSLOCALDIR + "{dataType}/{datasetName}/filtered.sifit_cell_names", dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),
        expand(SIFITTRUEMONOVARSNVSTRUEPARAMSLOCALDIR + "{dataType}/{datasetName}/filtered.sifit_data", dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),
        expand(SIFITTRUEMONOVARSNVSTRUEPARAMSLOCALDIR + "{dataType}/{datasetName}/true_out", dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES),
        expand(SIFITTRUEMONOVARSNVSTRUEPARAMSLOCALDIR + "{dataType}/{datasetName}/filtered.sifit_data_mlTree.newick", dataType=SIMUDATATYPES, datasetName=SIMUDATASETNAMES)