Also import profile read counts and percentages

bin/import_jovian_output.py

@@ -3,6 +3,8 @@
 # Import the output of Jovian, that is needed to screen for
 # species and sequences, into another directory. This includes
 # trimmed reads, filtered scaffolds and classification tables.
+# It also import other useful output files, such as sample composition
+# graphs, Krona charts, and tables of taxonomic abundances.
 #
 # Example use:
 # $ python3 import_jovian_output.py -i ../Jovian/ -o ./ -m move
@@ -529,7 +531,8 @@ def main():
 
     print("Trying to copy extra files:")
     print("pipeline_parameters.yaml, multiqc.html,")
-    print("Sample_composition_graph.html, Krona.html and heatmaps.")
+    print("Sample_composition_graph.html, Krona.html, heatmaps,")
+    print("and profile_read_counts.csv and profile_percentages.csv.")
 
     try:
         shutil.copy2(
@@ -550,6 +553,14 @@ def main():
         )
         for heatmap in list(Path(main_input / "results" / "heatmaps").glob("*.html")):
             shutil.copy2(heatmap, Path(main_output / "data" / "raw" / "Jovian_report"))
+        shutil.copy2(
+            Path(main_input / "results" / "profile_read_counts.csv"),
+            Path(main_output / "data" / "raw" / "Jovian_report"),
+        )
+        shutil.copy2(
+            Path(main_input / "results" / "profile_percentages.csv"),
+            Path(main_output / "data" / "raw" / "Jovian_report")
+        )
 
     except:
         print("Could not copy all Jovian results files.")