reduced manuscript to figures

Snakefile

@@ -10,17 +10,19 @@ include: "rules/final_imputation_report.rule"
 
 
 
-rule manuscript:
+rule manuscript_figures:
     input:
         pop_report = rules.prepare_data_v1_1.output,
         posteriors = rules.fit_models_validation_v1_1.input,
         markdown   = "manuscript/manuscript.Rmd"
     output:
-        "output/v1.1/manuscript.docx"
+        "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'))"
+        Rscript scripts/manuscript_figures.R
+        zip -rm manuscript-figures.zip *.eps
+        mv manuscript-figures.zip output/v1.1/manuscript-figures.zip
         """