amend

dynamic_report/workflow/Snakefile

@@ -96,11 +96,8 @@ rule dynamic_report:
         rm -r .writable_template_copy # Problem is that this file is only removed if pipeline finishes. Should it be removed by onerror?
 
         # End script
-        test -f "{params.end_script}" && echo "running end script" && . {params.end_script} {batch_title} {output_directory}/report_{batch_title}.html 
+        test -f "{params.end_script}" && echo "running end script" && . {params.end_script} {batch_title} {output_directory}/report_{batch_title}.html || true
         
-        # Print the ass. Thanks to George Taiaroa.
-        echo "{params.text_box}"
-        cat "{base_variable}/resources/ass.txt"
     """
 
 
@@ -109,9 +106,8 @@ def format_sections():
     """
     file = f"{output_directory}/tables/{batch_title}__sections.tsv"
     if os.path.exists(file): 
-        df_sections = pd.read_csv(file, sep = "\t")
-        df_sections = df_sections.rename(columns={"render": "render_emoji"})
-        df_sections['render'] = [i.encode('ascii',errors='ignore').decode() for i in df_sections['render_emoji']]
+        df_sections = pd.read_csv(file, sep = "\t").rename(columns={"render": "render_emoji"})
+        df_sections['render'] = [i.encode('ascii', errors='ignore').decode() for i in df_sections['render_emoji']]
         return df_sections[["section", "n / expected", "render"]].to_string(index = False)
     else: # If something messes up the report so bad that this file is not written. 
         return f"(could not read {file})"