...

Snakefile

@@ -205,17 +205,18 @@ rule imputation_report:
         rules.post_process_imputations.output,
         markdown = "reports/imputations.Rmd"
     output:
-        pdf     = "output/{version}/imputations_{model}.pdf",
-        figures = "output/{version}/imputations_{model}_figures.zip"
+        pdf     = "output/{version}/gose_imputations_{model}.pdf",
+        figures = "output/{version}/gose_imputations_{model}_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\\", imputations = \\"../output/v1.1/data/imputation/{wildcards.model}/df_gose_imputed.csv\\"))"
+        Rscript -e "rmarkdown::render(\\"{input.markdown}\\", params = list(data_dir = \\"../output/{wildcards.version}/data\\", imputations = \\"../output/v1.1/data/imputation/{wildcards.model}/df_gose_imputed.csv\\"))"
+        mv reports/imputations.pdf {output.pdf}
         mv reports/figures.zip {output.figures}
         """
 
 # define corresponding target rule for ease of use
 rule impute_msm_v1_1:
     input:
-        pdf     = "output/v1.1/imputations_msm.pdf",
-        figures = "output/v1.1/imputations_msm_figures.zip"
+        pdf     = "output/v1.1/gose_imputations_msm.pdf",
+        figures = "output/v1.1/gose_imputations_msm_figures.zip"