amend

asscom2

@@ -70,7 +70,7 @@ OPTIONS
           - fast        (Only rules that complete within a few seconds. Useful for testing.)
           - isolate     (Only rules that are relevant for genomes of isolate origin.)
           - meta        (Only rules that are relevant for genomes "MAGs" of metagenomic origin.)
-          - report      (Re-renders the report)
+          - report      (Re-renders the report.)
         
     --dry-run
         Run a "dry run": Shows what will run without doing it.
@@ -161,7 +161,7 @@ trailing_arguments = sys.argv[1:]
 trailing_arguments_concatenated = " ".join(trailing_arguments)
 logger.debug(f"The concatenated trailing arguments are {trailing_arguments_concatenated}")
 
-command = f"snakemake --snakefile \"{ASSCOM2_BASE}\"/workflow/snakefile --profile \"{ASSCOM2_PROFILE}\" --configfile \"{ASSCOM2_BASE}\"/config.yaml  " + trailing_arguments_concatenated
+command = f"snakemake --snakefile \"{ASSCOM2_BASE}\"/workflow/Snakefile --profile \"{ASSCOM2_PROFILE}\" --configfile \"{ASSCOM2_BASE}\"/config/config.yaml  " + trailing_arguments_concatenated
 logger.debug(f"Command to run is\n{command}")
 
 

workflow/Snakefile

@@ -384,10 +384,7 @@ report_call = f"""
         && snakemake \
             --snakefile "$ASSCOM2_BASE/dynamic_report/workflow/Snakefile" \
             --profile "$ASSCOM2_PROFILE" \
-            --config results_directory="$(pwd -P)/{results_directory}" base_variable="{base_variable}" batch_title="{batch_title}" version_string="{__version__}"
-    ) || ( 
-        echo "Info: Not calling the dynamic_report as either the flag or metadata is missing. Run a rule that mandates a report section to generate the report.";
-        exit 1;
+            --config results_directory="$(pwd -P)/{results_directory}" base_variable="{base_variable}" batch_title="{batch_title}" version_string="{__version__}" 
     )
     """