...

Snakefile

@@ -221,3 +221,25 @@ rule impute_msm_v1_1:
     input:
         pdf     = "output/v1.1/gose_imputations_msm.pdf",
         figures = "output/v1.1/gose_imputations_msm_figures.zip"
+
+
+
+
+rule manuscript:
+    input:
+        pop_report = rules.prepare_data.output,
+        posteriors = rules.model_posteriors.input,
+        markdown   = "manuscript/manuscript.Rmd"
+    output:
+        pdf     = "output/{version}/manuscript.docx",
+        figures = "output/{version}/manuscript_figures.zip"
+    shell:
+        """
+        mkdir -p output/{wildcards.version}
+        Rscript -e "rmarkdown::render(\\"{input.markdown}\\", output_dir = \\"output/{wildcards.version}\\", params = list(data_dir = \\"../output/{wildcards.version}/data\\", config_file = \\"../config.yml\\"))"
+        mv manuscript/figures.zip {output.figures}
+        """
+
+rule manuscript_v1_1:
+    input:
+        "output/v1.1/manuscript.docx"