fixed quoting issue

Snakefile

@@ -34,7 +34,7 @@ rule prepare_data:
     shell:
         """
         mkdir -p output/{wildcards.version}/data
-        Rscript -e "rmarkdown::render('{input.markdown}', output_dir = 'output/{wildcards.version}', params = list(datapath = '../data/{wildcards.version}', max_lab_days = {config[max_lab_days]}, seed = {config[seed]}))"
+        Rscript -e "rmarkdown::render(\\"{input.markdown}\\", output_dir = \\"output/{wildcards.version}\\", params = list(datapath = \\"../data/{wildcards.version}\\", max_lab_days = {config[max_lab_days]}, seed = {config[seed]}))"
         mv reports/*.rds output/{wildcards.version}/data
         mv reports/figures.zip {output.figures}
         """
@@ -119,7 +119,7 @@ rule model_assessment:
     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'))"
+        Rscript -e "rmarkdown::render(\\"{input.markdown}\\", output_dir = \\"output/{wildcards.version}\\", params = list(data_dir = \\"../output/{wildcards.version}/data\\", config_file = \\"../config.yml\\"))"
         mv reports/figures.zip {output.figures}
         """