DelSIEVE_benchmark_pipeline/remote_sifit_true_monovar.snake at main · szczurek-lab/DelSIEVE_benchmark_pipeline · GitHub

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"""
Run SIFIT with data from MONOVAR with true parameters remotely.
"""

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


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

SNAKEMAKEDIR = get_abs_working_dir()


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

rule all:
    input:
        expand(SIFITGITSKELETONTRUEMONOVARREMOTEDIR + config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/true_out", dataType=config["benchmark"]["simulation"]["dataTypeNames"], datasetName=config["benchmark"]["simulation"]["datasetNames"]),
        expand(SIFITGITSKELETONTRUEMONOVARREMOTEDIR + config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/data_mlTree.newick", dataType=config["benchmark"]["simulation"]["dataTypeNames"], datasetName=config["benchmark"]["simulation"]["datasetNames"])
    output:
        protected(config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "done")
    params:
        dataDir=SIFITGITSKELETONTRUEMONOVARREMOTEDIR,
        remoteUserName=config["benchmark"]["git"]["remote"]["userName"],
        remoteUserEmail=config["benchmark"]["git"]["remote"]["userEmail"],
        folderName=config["benchmark"]["paramTypes"]["fromTrueParamsDir"],
        commitMSG="[remote] added results of " + config["benchmark"]["phyloInf"]["fromTrueMonovarDir"].rstrip("/")
    shell:
        "cd {params.dataDir}; "
        "git config --local user.name \"{params.remoteUserName}\"; "
        "git config --local user.email \"{params.remoteUserEmail}\"; "
        "git add {params.folderName}; "
        "git commit -m \"{params.commitMSG}\"; "
        "cd {SNAKEMAKEDIR}; "
        "touch {output}"

# Rule: copy data from git repository to local folder
rule copyDataFromGit2Local:
    input:
        data=SIFITGITSKELETONTRUEMONOVARREMOTEDIR + config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/data",
        cellNames=SIFITGITSKELETONTRUEMONOVARREMOTEDIR + config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/cell_names"
    output:
        dataTrueParams=protected(config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/data"),
        cellNamesTrueParams=protected(config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/cell_names")
    shell:
        "cp -f {input.data} {output.dataTrueParams}; "
        "cp -f {input.cellNames} {output.cellNamesTrueParams}"

# Rule: run SIFIT with TRUE parameters and SNVs called by Monovar with true parameters on remote server
rule runSifitWithTrueMonovarSNVsTrueParams:
    input:
        data=config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/data",
        cellNames=config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/cell_names"
    output:
        out=protected(config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/true_out"),
        tree=protected(config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/data_mlTree.newick")
    params:
        sifit=config["tools"]["sifitRemote"],
        loops=config["fineTune"]["sifit"]["loops"],
        fp=config["benchmark"]["analysis"]["effSeqErrRate"],
        fn=config["benchmark"]["analysis"]["adoRate"],
        cellNum=lambda wildcards, input: get_item_num(input.cellNames),
        siteNum=lambda wildcards, input: get_line_num(input.data)
    shell:
        "java -jar {params.sifit} "
        "-m {params.cellNum} "
        "-n {params.siteNum} "
        "-fp {params.fp} "
        "-fn {params.fn} "
        "-iter {params.loops} "
        "-df 1 -ipMat {input.data} "
        "-cellNames {input.cellNames} "
        "&>{output.out}"

# Rule: copy results from remote server to local server
rule copyResultsToLocal:
    input:
        outTrueParams=config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/true_out",
        treeTrueParams=config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/data_mlTree.newick"
    output:
        outTrueParams=protected(SIFITGITSKELETONTRUEMONOVARREMOTEDIR + config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/true_out"),
        treeTrueParams=protected(SIFITGITSKELETONTRUEMONOVARREMOTEDIR + config["benchmark"]["paramTypes"]["fromTrueParamsDir"] + "{dataType}/{datasetName}/data_mlTree.newick")
    shell:
        "cp -f {input.outTrueParams} {output.outTrueParams}; "
        "cp -f {input.treeTrueParams} {output.treeTrueParams}"