singularity: "container.sif"

configfile: "config.yml"

include: "rules/fit_model_validation.rule"

include: "rules/final_imputation_report.rule"





rule create_manuscript_v1_1:
    input:
        pop_report = rules.prepare_data_v1_1.output,
        posteriors = rules.fit_models_validation_v1_1.input,
        markdown   = "manuscript/manuscript.Rmd"
    output:
        pdf     = "output/v1.1/manuscript.docx",
        figures = "output/v1.1/manuscript_figures.zip"
    shell:
        """
        mkdir -p output/v1.1
        Rscript -e "rmarkdown::render(\\"{input.markdown}\\", output_dir = \\"output/v1.1\\", params = list(data_dir = \\"../output/v1.1/data\\", config_file = \\"../config.yml\\"))"
        mv manuscript/figures.zip {output.figures}
        """





rule impute_population_wide_msm_v1_1:
    input:
        "output/v1.1/gose_imputations_msm.html",
        "output/v1.1/gose_imputations_msm_figures.zip"