singularity: "container.sif"

configfile: "config/snakemake.yml"



rule download:
    input:
        config = "config/snakemake.yml",
        links  = "config/tbl_download_links.csv",
        script = "scripts/download-data-table.R"
    output:
        csv    = expand("{datapath}/tbl_gose_imputation.csv",
            datapath = config["datapath"])
    shell:
        """
        mkdir -p {config[datapath]}
        Rscript scripts/download-data-table.R $NEUROBOT_USR $NEUROBOT_API {config[neurobot_staging_version]} gose_imputation
        mv tbl_gose_imputation.csv {output.csv}
        """



rule check_inputs:
    input:
        csv    = expand("{datapath}/tbl_gose_imputation.csv",
            datapath = config["datapath"]
        ),
        script = "scripts/check-inputs.R"
    shell:
        """
        Rscript scripts/check-inputs.R {config[datapath]}/tbl_gose_imputation.csv
        """



rule impute:
    input:
        config = "config/snakemake.yml",
        csv    = expand("{datapath}/tbl_gose_imputation.csv",
            datapath = config["datapath"]
        ),
        rmd    = "imputation-report.Rmd"
    output:
        html   = "output/imputation-report.html",
        csv    = "output/tbl_imputed_gose.csv"
    shell:
        """
        Rscript scripts/check-inputs.R {config[datapath]}/tbl_gose_imputation.csv
        mkdir -p output
        Rscript -e "rmarkdown::render(\\"{input.rmd}\\")"
        mv tbl_imputed_gose.csv {output.csv}
        mv imputation-report.html {output.html}
        """